Using the implicit membrane model IMM1

GMIN can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis (1). To use this, first update and compile charmm and GMIN as described by Compiling_GMIN_with_CHARMM.

Since the use of a membrane introduces directionality to the system, previous parameters specifying orientation and spacial position become important. Rotation can be defined in the data file using the terms

CHPMAX  0.4
CHPMIN  0.2
CHNMAX  10
CHNMIN  0

These parameters are described in the GMIN documentation. Note that if including these terms in the data file, the directory must also contain a file entitled segment.tomove which contains the single character

1

The system can be translated so that the centre-of-mass lies at the origin after every quench. This is achieved by including in the data file the term

CENTRE

At present, CENTRE causes convergence issues as moving back to z=0 actually changes the energy. It is advised the CENTREXY is used instead (see below).

Two new terms have been included for use with the implicit membrane. The coordinates of the centre of mass of the system before the initial quench can be specified using:

SETCENTRE <i>x</i> <i>y</i> <i>z</i>

Specifying x y z as 0.0, 0.0, 0.0 will set the centre of mass at the origin and hence the centre of the membrane. A protein can be moved out of the membrane by altering the z coordinate.

Secondly, CENTREXY moves the protein back to (0,0,z) i.e. it preserved the z-coordinate. This solves the convergence problem mentioned above when using CENTRE.

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A shorter dump interval is recommended as system size (and therefore time/quench) increases. To restore a run, you need the RESTORE keyword. Here are two excerpts from example data files to demonstrate:

Original data file:

...
DUMPINT 100
STEPS 10000
SAVE 100
...

data file for restarted run:

...
DUMPINT 100
RESTORE GMIN.dump
STEPS 15000
SAVE 100
...

The number of steps in the new data file should always be greater than in the original. In this case, the run is being restarted for a further 5000 quenches - 10000 + 5000 = 15000! The makerestart script does a lot of this for you.

What if I want to change the value of SAVE?

For large systems, it is nice to have the flexibility to change the number of structures that are tightly converged and dumped at the end of a run. This is because final quenches often take a long time, and you may only need to see one or two structures at the start of a long series of restart runs. If your dump file was generated by a version of GMIN compiled from the repository after 30/9/2008, you can do this by simply changing the value of SAVE in the new data file. If not, you need to make a simple modification to the dump file before you use it. Open the dump file in an editor e.g. vi:

vi GMIN.dump

In the new format, there is an extra line in the dump file which details the number of structures saved in the previous run. You need to input this manually if you have an old dump file, otherwise it will not be read in correctly. Here is an example, first the original - old dump file:

 steps completed J1 in mc
   13000
COORDS
run number        1
       22.174000000000000       83.915460000000000       47.511220000000000
       21.352510000000000       82.452780000000000       47.773840000000000
       22.240000000000000       82.880000000000000       47.440000000000000
...

Here, 13000 quenches have been done. Looking at the old data file above - we know that 100 structures were saved. This info must now be included in the dump file. The modification is performed as follows:

 steps completed J1 in mc
   13000
     100
COORDS
run number        1
       22.174000000000000       83.915460000000000       47.511220000000000
       21.352510000000000       82.452780000000000       47.773840000000000
       22.240000000000000       82.880000000000000       47.440000000000000
...

With this change done, you are now free to set SAVE to anything you'd like for the restart run.