[gmx-users] DNA splitting in simulations

[Justin Lemkul]

On 6/27/17 7:11 AM, Sergio Manzetti wrote:
> Thanks for the funny message, but I dont think this is recollection of imaginary character: just tried with one Tcppl group (SOL) :
> 
> Fatal error:
> 1435 atoms are not part of any of the T-Coupling groups
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> 

If you're only trying to couple the water (SOL) to a thermostat, then naturally 
grompp is going to tell you that you're doing something that is not sensible. 
It is *not* telling you "you need to set every type of molecule to its own 
group," it is telling you that what you're doing is fundamentally unphysical by 
coupling some atoms but not all.  Normally one would set "System" or at most two 
separate groups for the solute (DNA) and the combined solvent (a merged group of 
water and ions, created with make_ndx).  I know at least my tutorial walks you 
through this.

-Justin

> 
> 
> 
> Sergio Manzetti
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]
> 
> 
> 
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Tuesday, June 27, 2017 3:11:15 PM
> Subject: Re: [gmx-users] DNA splitting in simulations
> 
> On 6/27/17 7:05 AM, Sergio Manzetti wrote:
>> Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the email, grompp wanted equal number of tcouplings as groups in the top file.
>>
> 
> That's not true and what you're doing is not sensible. If you're having a
> problem, please provide an exact error message from grompp, not what's filtered
> through your recollection :)
> 
> -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

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