[gmx-users] number of coordinates does not match after POSRES

[Justin Lemkul]

On 6/8/17 12:23 AM, Simon Kit Sang Chu wrote:
> Hi Justin,
> 
> Thanks for your advice. Since we are using a forcefield which could only
> incorporate with gromacs 3.3.1, we have no choice but to prepare the system
> in the old version, then run it with the latest version of gromacs.
> 

The only change in force fields between 3.3.x and now is a reorganization into 
directories.  It's a trivial adjustment to make.  You'll get much faster 
performance and thousands of bug fixes if you update to something modern.

> Yes, indeed the option should be with -DPOSRES instead. And the topology
> file should #include chainA-pace.top, then chainA_posres.itp in this
> alternative manner. It seems that writing all chainA chainB.top first and
> all pores.itp later would not do it. Please tell me if I am wrong.
> 

Right, position restraints are on a per-moleculetype basis.  Any 
[position_restraints] directive applies to the [moleculetype] that immediately 
precedes it in the topology.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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