Re: [gmx-users] ci variable range error in parallel but NOT in serial

dtmirij wrote: For the two processor job: From my .mdp file, the pressure input data is as follows: _ ; Pressure coupling = Pcoupl = Berendsen Pcoupltype = Anisotropic ; Time constant (p

Re: [gmx-users] Polarizability

Jones de Andrade wrote: Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. lots of plans, but no promises. we really don't want to raise any e

Re: [gmx-users] Two polypeptides in one box

Am Samstag, 19. Mai 2007 schrieb Sheyore Omovie: > I want to simulate interaction between two polypeptides in one box. I have > read Tsjerk response to a similar question. However, i dont know just how > to implement it, i.e how do I position two pdb files using editconf and > create one pdb file.

Re: [gmx-users] Polarizability

Hi David. I had no idea that gromos was using it. Also, just had a few clues that maybe charmm was. All amber clues however points towards a different model. I have a few concerns about "directioning" (really sure that this is the wrong word, if exists) that a shell model polarizability would ma

[gmx-users] What molecule generator should be used if using GROMOS Force Field?

Hi, Everyone, If I use GROMOS force field, what molecule generator, specially the topology generation, should I use (just like for gromacs force field, there is PRODRG)? I have tried to convert gromacs topology to GROMOS topology. The problem is that some atom type like "CS2" in PEO does noe exi

[gmx-users] pH

Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is equal to zero. no dissociation.

Re: [gmx-users] Polarizability

Jones de Andrade wrote: Hi David. I had no idea that gromos was using it. Also, just had a few clues that maybe charmm was. All amber clues however points towards a different model. They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually

Re: [gmx-users] pH

Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is eq

Re: [gmx-users] What molecule generator should be used if using GROMOS Force Field?

WU Yanbin wrote: Hi, Everyone, If I use GROMOS force field, what molecule generator, specially the topology generation, should I use (just like for gromacs force field, there is PRODRG)? I have tried to convert gromacs topology to GROMOS topology. The problem is that some atom type like "C

Re: [gmx-users] pH

20 maj 2007 kl. 20.59 skrev David van der Spoel: Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the st

[gmx-users] Re: gmx-users Digest, Vol 37, Issue 73

From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 20 May 2007 20:59:45 +0200 Subject: Re: [gmx-users] pH Dmitriy Golubovsky wrote: > Dear Guru! > > have you got any idea, on what how to calculate pH. for the system? > i'm solving a promblem of coil-gl

Re: [gmx-users] Re: gmx-users Digest, Vol 37, Issue 73

Dmitriy Golubovsky wrote: From: David van der Spoel <[EMAIL PROTECTED] > To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Date: Sun, 20 May 2007 20:59:45 +0200 Subject: Re: [gmx-users] pH Dmitriy Golubovsky wrote: > Dear

Re: [gmx-users] pH

> > 20 maj 2007 kl. 20.59 skrev David van der Spoel: > >> Dmitriy Golubovsky wrote: >>> Dear Guru! >>> have you got any idea, on what how to calculate pH. for the system? >>> i'm solving a promblem of coil-globule transition for polymer. >>> do the topology for my structure(opls ff), do MD in water

[gmx-users] Re: Calculate individual force between each atom pair

Thanks for the suggestions. I have traced the calling sequence from do_force() to calculate LJ forces: do_force() -->force() -->do_nonbonded(). But in do_nonbonded() function of nonbonded.c file, if for general processor, it should have call gmx_nb_generic_kernel() function but this line is in f

Re: [gmx-users] pH

Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is eq

Re: [gmx-users] Polarizability

Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find i

[gmx-users] readxtc can not get coordinates without jump?

Hi, I faced one problem when reading xtc file. Assuming my xtc file is run.xtc and the last frame no. is 1 (time step=1ps, e.g, 10 ns in total), I want to see the coordinates of the whole system without jump at frame=1, and I used the command: (1)trjconv -f run.xtc -s run.tpr -o sys_1