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

shahab shariati shahab.shariati at gmail.com
Tue Sep 17 14:17:10 CEST 2013

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

> 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.

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