[gmx-users] Topol file for a bigger system
alexanderwien2k at gmail.com
Tue Mar 20 23:07:25 CET 2018
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
>> 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.
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?
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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