[gmx-users] .gro files generation for a certain time-step interval in a simulation

Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each at 1st ns, 2nd ns, 3rd ns and so on out from a

Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

gt; have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for > details on Hamiltonian REMD, especially the correct exchange criterion. > In their paper, they discuss in detail what you want to do, namely > Replica Exchange Umbrella Sampling. > > Marcus > > Huey Li

[gmx-users] REMD As A Function of Distance Between 2 Chains

Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the full

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

chain will do.. is that right? Thanks. On 02/11/2007, Mark Abraham <[EMAIL PROTECTED]> wrote: > > 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 pepti

[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

Re: [gmx-users] Problem putting 2 identical peptide chains in a simulation box

Hi Alok, Thanks for your email. Could you please explain in more detail? What do you mean by chain identifier? Many thanks. Best regards, Huey Ling On 26/10/2007, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Hello Huey Ling, > > Use different chain identifiers for different peptid

[gmx-users] Problem putting 2 identical peptide chains in a simulation box

Hi All, I am trying to put 2 identical peptide chains in a simulation box. However, gromacs tends to see both separate peptide chains as one. The following is the method that I used, please comment and correct me if I'm wrong. First, I translate the peptide to a certain distance. Then I

[gmx-users] Umbrella Sampling on peptides

Hi all, I am new in Gromacs. I used umbrella samplings in my simulations of 2 peptide chain with 1 positive charge and 1 negative charge on each chain. However, this 2 chain is sticking together even at high force (1ooo mol*nm^2). below is the pull.ppa file that i used: verbose = no runtype = umb

[gmx-users] Wall Potential

Hi all, I am trying to simulate multiple (2 or 3) tetrapeptides in a cage with Gromacs. However, I would like to constrain the peptides to the centre of the box by enforcing a wall potential in which each of the atoms of the peptide feels a repulsive potential with respect to the edge of the box