[gmx-users] Topol file for a bigger system

[Justin Lemkul]

On 3/20/18 6:06 PM, Alex wrote:
> On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 3/19/18 8:15 PM, Alex wrote:
>>
>>> Dear all,
>>>
>>> Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
>>> posrecase.itp out of a case.mol2 which contain only a single molecule of
>>> X.
>>>
>>> Also, using the "gmx insert-molecules" I can generate a bigger system
>>> containing 1000 molecule of X, for example to have case-1000.gro.
>>>
>>> Now, I was wondering how I can update the case.top and itp files for the
>>> new system? I am trying the "gmx x2top" but first of all it is really time
>>> consuming and also at the end it can not find the force fields for some of
>>> the atoms.
>>> (~> gmx x2top -f case-1000.gro -o out.top -r out.rtp)
>>>
>> Shouldn't it be as simple as updating the number of molecules in the .top
>> file to 1000?
>>
> You are right. Thank you.
>
>> There are no changes in .itp files, as only a .top keeps record of how
>> many of each species there are.
>>
> How about the posre.itp (the position restrain file)? The initial posre.itp
> only have the restrain only on the atoms of X molecule, whereas I might
> need to update it when the system has 1000X molecules.

This file requires no change. Position restraints are applied on a 
per-moleculetype level, so changes in global atom number are irrelevant.

> One more question:
> The gmx grompp in gromacs 2018, needs to have the positions of the atom for
> which restrain has been defined in posre.itp file to be read in "gmx grompp
> -f .. *-c conf.gro* *-r restraint.gro* .. ", am I right? then, should we
> update the restraint.gro file according to the conf.gro file? I means
> between each level of simulation (equalization, production .....) where gmx
> grompp is invoked we have to give a new restraint.gro file each time?

Yes.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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