Re: [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field

Thanks MARK for your reply,and your suggestion is very helpful. I don't write back until mdrun ends just now. I want to simulate DMSO property as it is cooled. So I put 500 DMSO moleculers in a box. Ref_t =300 ref_P=1. During the first 60ps ,the 500 DMSO moleculers seems to be diffusing outsi

Re: [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field

wang kelvin wrote: Thanks MARK for your reply,and your suggestion is very helpful. I don't write back until mdrun ends just now. I want to simulate DMSO property as it is cooled. So I put 500 DMSO moleculers in a box. Ref_t =300 ref_P=1. During the first 60ps ,the 500 DMSO moleculers se

[gmx-users] Energy minimization of a simple model without PBC

Hello, I'm totally new to gromacs and I've just started to make some simple things with simple models to expand them later. One of the models I concern is simply an isolated n-decane molecule in a large box without PBC. However, I start from quite bad geometry (e.g. bond lengths ca. 1.2-1.6A, angl

[gmx-users] small typo in ions.itp: LI+ atom is NA

I noticed this typo in ions.itp under the FF_OPLS section. It appears to have been present at least from 3.2.1 to 3.3.3 (the atom name for LI+ is NA) [ moleculetype ] ; molname nrexcl LI+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge ma

[gmx-users] Force field parameters in water or in vacuum?

Interesting, I was not aware of that. For the simulations that I was discussing, we did not see that type of collapse on the 10ns timescale, although we started from extended structures and used very high temperatures since we were only interested in using MD as one of many methods to generate a

[gmx-users] Re: 1-4 scaling problem?

Dear Anindita, There is good reason to keep this on the mailing list. I am happy to help, but you are misrepresenting the situation to say that you received no answer on the mailing list. In fact, you received quite a bit of assistance: http://www.gromacs.org/pipermail/gmx-users/2008-May/034064

[gmx-users] Hessian matrix calculation

Dear Users. Greetings. I want the perform hessian matrix with mdrun by option -mtx nm.mtx, But I didn't receive a out put nm.mtx I run this command after minimization of my structure. Can you help me to understand why mdrun didn't give me a output nm.mtx for Hessian but only traj.trr.

[gmx-users] 1-4 Scaling Problem?

Dear Sir, I am sufferering from a dmpc-bilayer-area shrinking problem. The fact is the experimental area at 300K is 59.6A2, where I am always getting 54A2 or 55A2 area. The dmpc_npat.pdb along with lipi.itp and dmpc.itp was taken from the Tieleman's site, and I tried to modify these with half-e

Re: [gmx-users] Hessian matrix calculation

Collins Nganou wrote: Dear Users. Greetings. I want the perform hessian matrix with mdrun by option -mtx nm.mtx, But I didn't receive a out put nm.mtx I run this command after minimization of my structure. Can you help me to understand why mdrun didn't give me a output nm.mtx for H