[gmx-users] Re: grompp for minimization: note & warning

[Justin Lemkul]

On 9/17/13 8:17 AM, shahab shariati wrote:
> Dear Justin
>
> Thanks for your time and consideration.
>
>> As I suggested before, visualize the output file and figure out what is
>> around atom 618 to cause such forces.
>
> I visualized output file (em.gro) by VMD. Atom 618 is  belonged to a dopc
> molecule (this dopc molecule is intact and is not broken). There are other
> dopc and cholesterol molecules around atom 618. How I understand what
> around this atom cause such forces.
> Excuse me. Please give me more explanation about your suggestion.

Usually when large forces arise, the cause is fairly obvious.  There will be 
some atom very close to the one on which the maximum force acts.  It may not 
always be obvious.

> May be, I did not understand your mean truly.
> Should I remove this dopc molecule and then run minimization again?
>

No.

>> PRODRG generates notoriously bad parameters, particularly the charges.
>
> I know this issue, charges and charges groups obtained from prodrg (in itp
> file) were compared with charges and charges groups in similar structures
> being in rtp file of gromos (because my drug is very similar to cytosine).
> Then I corrected them.
>

OK, that's a reasonable starting point.

-Justin

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

Justin A. Lemkul, Ph.D.
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

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