[gmx-users] 1-4 interaction, a distance greater than table size

Dear All, I'm simulating a DNA duplex using amber99p. starting the simulation(step 0) i face an error which tells: starting mdrun 'Protein in water' 50 steps,    500.0 ps. step 0Warning: 1-4 interaction between 136 and 179 at distance 96871502.536 which is larger than the 1-4 table size 2.0

[gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8

lds can be implemented, either as successive [dihedraltypes] of type 9 (since GROMACS 4.0, IIRC) or as multiple [dihedrals] of type 1 (since ages). Mark - Original Message - From: Amin Arabbagheri Date: Tuesday, November 2, 2010 17:06 Subject: [gmx-users] multiple torsio

[gmx-users] multiple torsions for one dihedral

Hi all, I'm using AMBER99p force field in GROMACS. In the AMBER forcefield for some dihedrals, there are several values, in which n values are different.  As an example, for C3-C3-N-C, I have C3-C3-N-C   .50  180.0  -4 C3-C3-N-C   .15  180.0  -3 C3-C3-N-C   .53  0.0   1 For the version 4, i

[gmx-users] multiple dihedrals

Hi all, I'm using ffamber99p ff in gromacs and now I have to use some additional parameters in the force field. Regarding to designation of proper dihedrals in AMBER, in some cases there are 2 or 3 dihedrals given for a specific torsion, in which parameters(e.g. angles) differ from each other 

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134

.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics:    1. (no subject) (Amin Arabbagheri)    2. Re: (no subject) (Justin A. Lemkul)    3. Re: (no subject) (Linus ?stberg)    4. Re: (no subject)

[gmx-users] (no subject)

Hi all, I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager. I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job. Thanks a lot