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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| − | energy state. One way of doing this is to run one step of minimisation with SANDER. |
+ | steps which is not the same at the evaluation of the lowest energy state. One way of doing this is to run one step of minimisation with SANDER. |
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) |
| − | -> ''' |
+ | -> '''inpcrd''' |
| + | (amber coordinates file) |
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| − | -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''' |
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| − | The names of 'numreplicas' and 'groupfile' can '''not''' be changed! All other files you can name |
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| + | (SANDER input file) |
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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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| + | cp coord.prmtop eval/prmtop |
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| − | tempi = 0, temp0 = 100.0, |
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| + | cp min.in eval/mdin |
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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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| + | 3. output files: |
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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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| + | '''mdinfo''' - Energy function output only |
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| − | nscm = 500, irest=1, |
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| + | '''mdout''' - Total Amber output |
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| − | ntave = 0, numexchg=100000 |
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| + | '''restrt''' - coordinates for restarting AMBER |
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| − | &end |
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Revision as of 16:33, 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. One way of doing this is to run one step of minimisation with SANDER.
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. output files:
mdinfo - Energy function output only mdout - Total Amber output restrt - coordinates for restarting AMBER