Re: [gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx

Qiao Baofu wrote: Hi, I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that "splitres" is to split group into residues, and "splitat" is to split group into atoms. But after I use them two, I found they are opsite. see the following example > splitres 3 Splitting group 3

[gmx-users] binding free energy calculations on charged ligands

Hello all,   I'm still trying to get the binding free energy for my ligands, and I now think I will have to do another simulation, since my first one used PME and I didn't record velocities in my trajectory.   But first I need some advice, since I can't find a paper which describes unambiguously

[gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx

Hi,I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that  "splitres" is to split group into residues, and "splitat" is to split group into atoms. But after I use them two, I found they are opsite. see the following example> splitres 3Splitting group 3 'MIL' into atoms> splitat 3Sp

RE: [gmx-users] The right way of killing Gromacs

From: kobi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: [gmx-users] The right way of killing Gromacs Date: Fri, 15 Sep 2006 11:33:27 +0200 Hello, the runtime of our cluster is unfortunately limited. Before mdrun is terminat

Re: [gmx-users] The right way of killing Gromacs

Hi, mdrun finishes on the next step when receiving TERM, and on the next multiple of nstxout when receiving USR1. On some systems, the USR1/SIGHUP is only sent to the parent MPI program, not the actual mdrun process, and then there isn't much we can do. In your case, try altering the si

[gmx-users] Re: Why RMSFs of some protein chains in my system are unreasonably large?

> are all the lysozymes treated as one protein? in that case it might be a PBC artifact. try doing the rmsf per molecule (by running the program 16> times) and then overlaying the result.   > are you trying to crystallize it?   >David.   Thank David. I just found that it was due to jumps i

Re: [gmx-users] Fatal error: Force field inconsistency

Quoting [EMAIL PROTECTED]: > > > Hello, > I had this error while trying to run a simulation for a small molecule > without > water and bilayer, I have included in the topol.top its parameters taken from > OPLS and its topology, since I did not created the topology with the pdb2gmx > I > did not i

[gmx-users] The right way of killing Gromacs

Hello, the runtime of our cluster is unfortunately limited. Before mdrun is terminated a USR1 signal is send, but this doesn't cause mdrun to writeout the current frame. Therefore most of the trajectory is lost. I'd like to write a skrip which converts the USR1 sinal to some other signal. The q

RE: [gmx-users] Surface Tension Calculation

write g_energy 6 0 enter the number 6 is just the corresponding to the surface tension, it can be any one. Quoting "Dallas B. Warren" <[EMAIL PROTECTED]>: > > I posted a question a few days ago regarding the > > calculation of the surface tension of a lipid bilayer in > > Gromacs. The respon

[gmx-users] MPI version on parallelknoppix live CD

Hi gromacs users. The there's a new release of the parallelknoppix live CD out that has a single precision, mpi-enabled version of gromacs installed. You can use this CD to set up a cluster and be running gromacs with MPI in about 10 minutes. The gmxdemo/demo file has been modified to allow you to