Re: [gmx-users] queue up simulations

sarbani chattopadhyay wrote: hi, I want to know is there any way to 'queue up mdrun jobs' so that once one job is finished, the next starts automaticaly? yes. check the docs for your queueing system. e.g. Torque, or Gridengine. Thanks in advance.

Re: [gmx-users] problems with opls_

i checked it but the what is the atomtype for opls_064 for? thanks --- David van der Spoel [EMAIL PROTECTED] wrote: huan wrote: i am a new user of Gromacs and i would like to knoe the opls for C, =O, and -O in RCOOR'. i tried it many times but i still fail to get the proper

[gmx-users] Fwd: trjconv help

  Note: Forwarded message attached -- Original Message -- From: sarbani chattopadhyay [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: trjconv help ---BeginMessage---  hi, I had run MD simulations where the output control parameters were nstxout=250 nstvout= 1000

Re: [gmx-users] problems with opls_

Check out ffoplsaanb.itp Tom --On Friday, October 26, 2007 01:05:46 -0700 huan [EMAIL PROTECTED] wrote: i checked it but the what is the atomtype for opls_064 for? thanks --- David van der Spoel [EMAIL PROTECTED] wrote: huan wrote: i am a new user of Gromacs and i would like to

[gmx-users] Re: trjconv help

sarbani chattopadhyay wrote: hi, I had run MD simulations where the output control parameters were nstxout=250 nstvout= 1000 nstenergy=100 Due to this the '.trr' file is very large. I want to compress this file so that xyz coordinates are stored every 1000 steps,

[gmx-users] constraining two diff molecules removes LJ interaction?

This is my first post to this list, so a warm hello to everybody! I want to constrain the distance between two atoms in different molecules (two diff proteins, in complex). So, I defined both molecules in the same [ moleculetype ] and added an extra [ bonds ] line: 216 6465 6 0.400 300.00

[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

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

Quoting Huey Ling Tan [EMAIL PROTECTED]: 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

[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?

Dear Chris, I have ran the equilibration run till 225ps but water molecule are not ready to stay at my desirable place :-( , I mean to say still I am getting uneven distribution of water moleculers over lipid head groups. Even after changing 0 to 4.5e-5. I also suggested that you change ref_p

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

Hello Huey Ling, Use different chain identifiers for different peptides. Then pdb2gmx will not create any bond between them. Regards, Alok 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.

[gmx-users] PBC, lincs and bonds breaking

I am trying to simulate my own structure based simulation using 3.3.2. I have developed the forcefield and it works fine without periodic boundary conditions. When I use pbc=xyz atoms that are connected in the [bonds] section of the topology get broken. What happens is 1 of the two atoms will

Re: [gmx-users] constraining two diff molecules removes LJ interaction?

This is my first post to this list, so a warm hello to everybody! I want to constrain the distance between two atoms in different molecules (two diff proteins, in complex). So, I defined both molecules in the same [ moleculetype ] and added an extra [ bonds ] line: 216 6465 6 0.400

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 peptides.

Re: [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

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? See http://wiki.gromacs.org/index.php/Multiple_Chains Mark ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] PBC, lincs and bonds breaking

I am trying to simulate my own structure based simulation using 3.3.2. What sort of structure? I have developed the forcefield and it works fine without periodic boundary conditions. When I use pbc=xyz atoms that are connected in the [bonds] section of the topology get broken. What

Re: [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

Hi I seem to be doing something wrong here, but cannot figure out what. - I have run a 200 ps NVT simulation for a lipid bilayer on 4 processors using the gromacs-3.3.1 build. - The last frame from the NVT simulation was used in conjunction with a newly written .mdp file to restart the

[gmx-users] PBC, lincs and bonds breaking

* I am trying to simulate my own structure based simulation using 3.3.2. * What sort of structure? RNA with a ligand (the ligand is the trouble) * I ** have developed the forcefield and it works fine without periodic boundary ** conditions. When I use pbc=xyz atoms that are connected in the