[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

Dear users, I' d like to know if I need to check the npt.gro file time by time? I mean is it possible for npt.gro file to reach the equilibrated state and then again become unequilibrated? Thanks for your suggestions. Sincerely, Shima From: Mark Abraham

[gmx-users] Multiplicity of a dihedral

Hello, How is the multiplicity of a dihedral determined? I know that it is related to the number of minima, but then how could we determine the number of minima? Is it with chemical intuition or with QM calculations? My molecule has several rings, which makes it not possible to calculate

Re: [gmx-users] Decreasing of the box size during membrane protein simulation

On 1/29/13 11:57 PM, James Starlight wrote: Justin, with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0 I've obtained decreae from 10 to 8.5. So it might be concluded that the observable is cut-off

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

On 1/30/13 6:01 AM, Shima Arasteh wrote: Dear users, I' d like to know if I need to check the npt.gro file time by time? I mean is it possible for npt.gro file to reach the equilibrated state and then again become unequilibrated? Unlikely, unless there's something wrong with your run

Re: [gmx-users] Decreasing of the box size during membrane protein simulation

Great discussion! While (seemingly) small changes in cut-off can give considerable performance improvements and therefore it is worth considering such tweaks in simulation settings, these finding highlight the importance of not changing settings blindly. Cheers, -- Szilárd On Wed, Jan 30,

[gmx-users] Error in BlueGene

Hello, I am having some problems to run my system in a bluegene cluster. I am running a bilayer simulation. The simulation runs very well in my local cluster. After 50ns of simulation on my local cluster with 8 nodes, I got the configurations and tried to run it in a bluegene with 512 nodes.

Re: [gmx-users] Multiplicity of a dihedral

On Wed, Jan 30, 2013 at 2:17 PM, Jong Wha Lee jongwh...@postech.ac.krwrote: Hello, How is the multiplicity of a dihedral determined? I know that it is related to the number of minima, but then how could we determine the number of minima? Is it with chemical intuition or with QM

Re: [gmx-users] Error in BlueGene

Mark, Thank you for your answer. I did an energy minimization with the file em.mdp (below) and then I did a 40 ns simulation with the same md.mdp I send before. These two steps were done in my local cluster. After that I took the configuration for the simulation in the bluegene and I got

Re: [gmx-users] drug topology file

On 1/30/13 3:27 PM, az kalsom wrote: hi, i wanted to know, what s simple way to correct the topology generated by PROGRG server i have read the paper mentioned in tutorial , but still i am nt able to correct the file please help me, should all CH3 CH2 charge ne made zero ? Not

[gmx-users] hi

hey have a look http://www.com-im6.net/finance/ Kowsar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

Re: [gmx-users] Error in BlueGene

Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try

[gmx-users] Bus error (core dumped)

Dear GROMACS experts, I run mdrun with this command: //mdrun -ntomp 8 -ntpi 1 -v -s em.tpr -deffnm em After Step 67, it was terminated with a Bus error (core dumped). Can anyone please explain this? Thanking you in advance. -- View this message in context: