On 3/20/18 6:06 PM, Alex wrote:
On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul <jalem...@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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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