[gmx-users] Output center of mass of each molecules in a system.

[Justin Lemkul]

On 6/8/17 12:19 PM, Christopher Neale wrote:
> make an index file with gmx make_ndx and then script it to create an index for each water molecule, e.g.:
> 
> 
> gmx make_ndx -f my.gro -o index.ndx << EOF
> 
> $(for((i=1;i<=100;i++)); do echo r${i}; done)
> 
> q
> 
> EOF
> 
> 

Even easier:

splitres (number of desired group)

-Justin

> then you can likewise script the input to gmx traj
> 
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Li, Shi <sli259 at g.uky.edu>
> Sent: 08 June 2017 11:26:46
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Output center of mass of each molecules in a system.
> 
> Dear GMX users,
> 
> I want to output the center of mass of each molecule in my simulation box.
> I think I should use gmx traj, with -com option. But this only gave me the
> center of mass for the whole system. If my system only contains 100 same
> solvent molecules, is there a method to output the center of mass for each
> individual molecule in the system?
> 
> Thank you for any help!
> Shi
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-- 
==================================================

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

==================================================