[gmx-users] (no subject)

 hi, I want to extend my run, for which I will have to use 'tpbconv' command.But this time I want to change the frequencies in which the energies,velocities and 'xyz' coordinates will be written to the trajectory file. Is there any way to do it? Thanks in advance.___

[gmx-users] gramicidin A

hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. Reading the earlier mail wjich states that: It's not too difficult to add a new residue to the topology database. Have a look in the file ff.rtp, where is the force field you are using. You can proba

Re: [gmx-users] Converting PDB to gromacs (Hydrogen problems)

Craig Schwartz wrote: Hey Gromacs Users, I am trying to convert the zwitterionic form of glycine into a top and gro file from the pdb, while I appear to be able to do this with some efficiency by PRODRG is there a way to do this that keeps all my hydrogens in the same locations? Yup. Se

[gmx-users] Converting PDB to gromacs (Hydrogen problems)

Hey Gromacs Users, I am trying to convert the zwitterionic form of glycine into a top and gro file from the pdb, while I appear to be able to do this with some efficiency by PRODRG is there a way to do this that keeps all my hydrogens in the same locations? This gets more complicated when I t

Re: [gmx-users] Problems in energygrps and tc-grps

Huey Ling Tan wrote: Dear gromacs users, I am simulating 2 identical peptide chains in a simulation box with water as solvent. To find the the equilibration, I wanted to calculate the energy of the peptide chains, separately, and then compare between them. To do that, I changed the en

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

himanshu khandelia wrote: I get bad scaling with 8 cpus. http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84 I'm not seeing how openmpi (the implementation) can be allocating cpus "depending on what options gromacs was originally compiled with". I do not see immediately how either,

Re: [gmx-users] Energy profiles for 2 separate peptide chains in a simulation box.

Huey Ling Tan wrote: The reason I want to do this is to compare the energy of both the peptide chains to find out whether they has reached equilibrium or not (it should be not much different between them as they are identical peptide chains). Therefore, I think by comparing the total energy for

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

I get bad scaling with 8 cpus. http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84 > I'm not seeing how openmpi (the implementation) can be > allocating cpus "depending on what options gromacs was originally > compiled with". I do not see immediately how either, but just seemed logical

[gmx-users] Problems in energygrps and tc-grps

Dear gromacs users, I am simulating 2 identical peptide chains in a simulation box with water as solvent. To find the the equilibration, I wanted to calculate the energy of the peptide chains, separately, and then compare between them. To do that, I changed the energygrps and tc-grps in my

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

himanshu khandelia wrote: Hi Mark, I do not want to request two separate 1-node jobs, so that I can make maximum use of the MAUI queue algorithm on our local cluster, which sometimes favors jobs which utilize more resources. So what about using 8-cpu jobs? I posted on this list, because some

Re: [gmx-users] Re: mdrun -rerun and box size bug not fixed?

Michel Cuendet wrote: Dear David and Berk, I am investigating further to understand why I don't get the same energies with -rerun. I will report next week. if you are using xtc files you will never get the same energies as in the original run because of the reduced precision in these files.

[gmx-users] Re: mdrun -rerun and box size bug not fixed?

Dear David and Berk, I am investigating further to understand why I don't get the same energies with -rerun. I will report next week. Thanks for your replies, Michel I just checked the 3.3.1 source code in md.c and the box is copied from the xtc file. I don't know where your problems could

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

Hi Mark, I do not want to request two separate 1-node jobs, so that I can make maximum use of the MAUI queue algorithm on our local cluster, which sometimes favors jobs which utilize more resources. I posted on this list, because someone here might have faced a similar problem before, and because

Re: [gmx-users] Energy profiles for 2 separate peptide chains in a simulation box.

The reason I want to do this is to compare the energy of both the peptide chains to find out whether they has reached equilibrium or not (it should be not much different between them as they are identical peptide chains). Therefore, I think by comparing the total energy for each of the peptide chai

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

himanshu khandelia wrote: Hi, I am requesting 2 4-cpu nodes on a cluster using PBS. I want to run a separate GMX simulation on each 4-cpu node. However, on 2 nodes, the speed for each simulation decreases (50 to 100%) if compared to a simulation which runs in a job which requests only one node.

Re: [gmx-users] Energy profiles for 2 separate peptide chains in a simulation box.

Huey Ling Tan wrote: Hi all, I am simulating 2 peptide chains in a box. May I know is it possible to calculate energy profile of each of the peptide chains with time steps? How will you define the energy of a peptide chain, and what will it tell you? Mark ___

[gmx-users] Energy profiles for 2 separate peptide chains in a simulation box.

Hi all, I am simulating 2 peptide chains in a box. May I know is it possible to calculate energy profile of each of the peptide chains with time steps? Thanks in advance. -- Best regards, Huey Ling ___ gmx-users mailing listgmx-users@gromacs

[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

Hi, I am requesting 2 4-cpu nodes on a cluster using PBS. I want to run a separate GMX simulation on each 4-cpu node. However, on 2 nodes, the speed for each simulation decreases (50 to 100%) if compared to a simulation which runs in a job which requests only one node. I am guessing this is becaus

Re: [gmx-users] POPC simulation

On Thu, Nov 01, 2007 at 12:36:33PM +, Moutusi Manna wrote: > Hi > I want to perform peptide + popc membrane simulation. I download > popc128a.pdb from > (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). > Before I introduce the peptide into the membrane, the wate

Re: [gmx-users] mdrun -rerun and box size bug not fixed?

I just checked the 3.3.1 source code in md.c and the box is copied from the xtc file. I don't know where your problems could come from. Berk. From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users]