[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

vivek sinha viveksinha20002 at gmail.com
Tue Jul 15 20:19:11 CEST 2014

Hey Justin,
I think I understood the problem. When I removed the solvent from inside
CNT, I kept the numbering of atoms just like before without actually making
a new strictly increasing order numbering. But now when I see that after
the energy minimization the new pdb file got arranged strictly by
increasing order.

As an example. After deleting atoms inside the CNT, my .gro file did not
had the atom no 6292, but after energy minimisation the em.gro file
contains the atom no 6292. This must have created a renumbering of the
atoms. Not good I suppose.
Please suggest what to do?

The concern is that whether to renumber the molecules after removing the
water from inside the CNT or not?

Thanking You,
Vivek Sinha

On Tue, Jul 15, 2014 at 9:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 7/14/14, 9:38 AM, vivek sinha wrote:
>> Hi Justin,
>> I dont have the periodic molecules so do I include anything in the .mdp
>> file? Also when I grompp this I get no warning or error or note. But when
>> I
>> mdrun it, I get
>> WARNING: Listed nonbonded interaction between particles 35 and 114
>> at distance 3f which is larger than the table limit 3f nm.
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason.
>> and then the program terminates after displaying a segmentation fault
>> error.
>> Please provide any valuable suggestions.
> Your system is blowing up.  It's a hard situation to diagnose with limited
> information, but something is almost certainly wrong with your topology.
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_
> Unstable_System
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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