Difference between revisions of "Evaluating different components of AMBER energy function with SANDER"
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===Editing Evaluating different components of AMBER energy function with SANDER=== |
===Editing Evaluating different components of AMBER energy function with SANDER=== |
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| − | After running AMBGMIN, |
+ | After running AMBGMIN (with 'DUMPSTRUCTURES', 'SAVE 5' set in GMIN 'data' file), it is informative to examine |
| + | the different components of the all-atom energy function. The AMBGMIN output contains averages over MD time |
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| − | The AMBGMIN output contains averages over MD time steps which is not the same at the evaluation of the lowest |
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| + | steps which is not the same at the evaluation of the lowest energy state, naturally. One can use SANDER to run one |
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| − | energy state. One way of doing this is to run one step of minimisation with SANDER. |
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| + | step of minimisation to generate the different components of the energy function. |
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This is easily done. Three input files are needed '''prmtop''', '''inpcrd''', and '''mdin''', along with the SANDER executable. |
This is easily done. Three input files are needed '''prmtop''', '''inpcrd''', and '''mdin''', along with the SANDER executable. |
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| − | -> ''' |
+ | -> '''prmtop''' - amber topology file |
| − | (number of repilcas) |
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| − | -> ''' |
+ | -> '''inpcrd''' - amber coordinates file |
| − | -A -i mdin.rep1 -o mdout.rep1 -c inpcrd.rep1 -p ./ala2.prmtop -r restrt.rep1 -x mdcrd.rep1 -inf mdinfo.rep1 |
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| + | -> '''mdin''' - SANDER input file |
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| − | The names of 'numreplicas' and 'groupfile' can '''not''' be changed! All other files you can name |
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| − | as you like. |
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| + | An easy way to do this is create an seperate directory via 'mkdir eval' |
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| − | mdin.rep*, inpcrd.rep* and ala2.prmtop define the other input files; all other files are for output. |
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| + | '''1. compile SANDER:''' |
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| − | The '''inpcrd.rep*''' and '''ala2.prmtop''' are the usual '''coordinate''' and '''topology files''', and '''mdin.rep*''' |
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| − | define the input for the MD for each replica: |
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| + | '''2. move files from GMIN output directory:''' |
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| − | REMD run 1 |
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| + | |||
| − | &cntrl |
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| + | cp min1.rst eval/inpcrd |
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| − | imin = 0, nstlim = 500, dt = 0.002, |
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| + | |||
| − | tempi = 0, temp0 = 100.0, |
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| + | cp coord.prmtop eval/prmtop |
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| − | ntt = 3, tol = 0.000001, gamma_ln = 5.0, |
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| + | |||
| − | ntc = 2, ntf = 1, ntb = 0, ntx = 5, |
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| + | cp min.in eval/mdin |
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| − | ntwx = 500, ntwe = 0, ntwr =500, ntpr = 500, |
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| + | |||
| − | cut = 99.0, igb = 0, saltcon=0.0, |
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| + | '''3. Run SANDER:''' |
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| − | nscm = 500, irest=1, |
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| + | |||
| − | ntave = 0, numexchg=100000 |
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| + | '''4. output files:''' |
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| − | &end |
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| + | |||
| + | Performed a sanity check between AMBGMIN and SANDER and the energies are the same. |
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| + | |||
| + | '''mdinfo''' - Energy function output only |
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| + | |||
| + | '''mdout''' - Total Amber output |
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| + | |||
| + | '''restrt''' - coordinates for restarting AMBER |
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| + | |||
| + | --[[User:mp466|mp466]] 17:03, 3 October 2009 (BST) |
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Latest revision as of 18:01, 3 October 2009
Editing Evaluating different components of AMBER energy function with SANDER
After running AMBGMIN (with 'DUMPSTRUCTURES', 'SAVE 5' set in GMIN 'data' file), it is informative to examine the different components of the all-atom energy function. The AMBGMIN output contains averages over MD time steps which is not the same at the evaluation of the lowest energy state, naturally. One can use SANDER to run one step of minimisation to generate the different components of the energy function.
This is easily done. Three input files are needed prmtop, inpcrd, and mdin, along with the SANDER executable.
-> prmtop - amber topology file
-> inpcrd - amber coordinates file
-> mdin - SANDER input file
An easy way to do this is create an seperate directory via 'mkdir eval'
1. compile SANDER:
2. move files from GMIN output directory:
cp min1.rst eval/inpcrd
cp coord.prmtop eval/prmtop
cp min.in eval/mdin
3. Run SANDER:
4. output files:
Performed a sanity check between AMBGMIN and SANDER and the energies are the same.
mdinfo - Energy function output only
mdout - Total Amber output
restrt - coordinates for restarting AMBER
--mp466 17:03, 3 October 2009 (BST)