[gmx-users] Fwd:

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[gmx-users] Fw:

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RE: [gmx-users] problem with result from g_rdf

Using g_dist I got the distance between the atom pair for which i need rdf. Made a histogram, using the default bin width used in gromacs. Then divide by 4*Pi*r^2 to normalize (where r is the distance between the pair). I expect my values to agree with that from g_rdf. While the graphs are exa

[gmx-users] non bonded interactions

I turned off all non bonded interaction using the following: energygrp_excl = SOL SOL SOL Protein_A SOL Protein_B Protein_A Protein_B (where Protein_A and Protein_B, are the 2 molecules (peptides) in the box) I assume this will not affect excluded volume i.e I do not expect to see distances l

RE: [gmx-users] non bonded interactions

turning off all other non bonded may accomplished this, I guess this is not possible. > From: [EMAIL PROTECTED]> Subject: Re: [gmx-users] non bonded interactions> > To: gmx-users@gromacs.org> Date: Sun, 10 Feb 2008 10:24:35 +0100> > On Fri, 8 > Feb 2008 20:27:35 -0500> Sheyo

RE: [gmx-users] non bonded interactions

s] non bonded interactions> To: gmx-users@gromacs.org> Date: Sun, 10 Feb 2008 10:24:35 +0100> > On Fri, 8 Feb 2008 20:27:35 -0500> Sheyore Omovie <[EMAIL PROTECTED]> wrote:> > > > I turned off all non bonded interaction using the following:> > > > en

RE: [gmx-users] Re: Putting more than one peptide

Another way arround it is to place all 5 peptides in a pdb file, separating each with TER ( be sure the coordinates of d atoms are not d same); before running editconf and genbox.> Date: Fri, 1 Aug 2008 14:41:34 +0300> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: [gmx-users] Re:

[gmx-users] Two polypeptides in one box

Hi gromacs users, 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. If possible I'll appreciate specifi

[gmx-users] Error with Energy minimisation

Hi, I was trying out the Ribonuclease S-peptide simulation in the online tutorial manual. I get the following error message when I try to do energy minimisation: ' Error: Need to obtain the job magic number in MXMPI_MAGIC' What could I have done wrong? I would appreciate any help. Regards John

Re: [gmx-users] Error with Energy minimisation

[gmx-users] Error with Energy minimisation Date: Sun, 20 May 2007 10:47:05 +1000 Sheyore Omovie wrote: Hi, I was trying out the Ribonuclease S-peptide simulation in the online tutorial manual. I get the following error message when I try to do energy minimisation: ' Error: Need to obta

[gmx-users] Polypeptide interaction

Hi gromacs users, I have succeeded in placing two polypeptides in a box. However my objective is to model the interaction between the central alpha c-atoms of both molecules. In particular the distance between them. My question is how do I implement distance between them before simulation, as th

[gmx-users] Coordinate file does not match topology

Dear gromacs users, While trying to preprocess my files with grompp, i got the ff error message: "Number of coordinates in coordinate file (b4em.gro, 2312) does not match topology (twopolypeptide.top, 2291)" How can I fix this? Regards John __

Re: [gmx-users] Coordinate file does not match topology

nal Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files wi

Re: [gmx-users] Coordinate file does not match topology

ke [ molecules ] Protein X SOL X K+ X Match the number there. Commands like grep SOL ABC.gro | wc or grep Mg ABC.gro | wc or grep POT ABC.gro | wc shall be your good companion. Regards, Yang Ye On 6/10/2007 8:42 AM, Sheyore Omovie wrote: Thanks, But this is my first real simulation, So I&

Re: [gmx-users] Coordinate file does not match topology

TED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Sun, 10 Jun 2007 23:02:29 +0800 On 6/10/2007 8:54 PM, Sheyore Omovie wrote: You're right, the total charge is zero. While cre

Re: [gmx-users] Coordinate file does not match topology

Spoel wrote: Sheyore Omovie wrote: Thanks Yang, Each of the residues in my *.gro have more H-atoms than in *.top. I added the 21 H-atoms in [molecules] section of *.top. But grompp still came up with the ff error: No such molecule type. Do i have to edit [moleculetype] section too? Rgds John

[gmx-users] potential energy =nan

I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong?

Re: [gmx-users] potential energy =nan

e on making the water flexible. Rgds John From: Mark Abraham <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing an Energy M

Re: [gmx-users] potential energy =nan

TOM41 O2 ALA A 6 8.599 3.832 -0.37 1 0 TER ENDMDL From: "Sheyore Omovie" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 11:44:32

[gmx-users] Step size too small

Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message fo

[gmx-users] job magic number in MXMPI_MAGIC

17 August 2007 19:02 +0200 Per Larsson <[EMAIL PROTECTED]> > wrote:> > > Hello!> >> >> > Check out> > > http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan> > > ge_in_energy._Converged_to_machine_precision.2C_but_not_to

RE: [gmx-users] Step size too small

; > Hope this helps> >> > Tom> >> > --On 17 August 2007 19:02 +0200 > Per Larsson <[EMAIL PROTECTED]> > > wrote:> >> >> Hello!> >>> >>> >> Check > out> >> http://wiki.gromacs.org/index.php/Errors#Stepsize_t

RE: [gmx-users] generation of the pdb file

I have used pymol to generate pdb files for simple polypeptides. You might want to check to see if it will meet your needs. Rgds John> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Date: Fri, 24 Aug 2007 07:48:27 +0800> Subject: [gmx-users] generation of the pdb file> > > Hi,> I am new i

RE: [gmx-users] Adding two peptides in a water box

_ Capture your memories in an online journal! http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

RE: [gmx-users] Adding two peptides in a water box

Hi Luciano, use the -label option to separately label the gro files (e.g A for the first peptide and B for the 2nd), before you cat them with an editor. pdb2gmx should now recognise them as separate molecules. Rgds John > Date: Sat, 8 Sep 2007 15:43:33 +0200> Subject: Re: [gmx-users] Adding two

[gmx-users] problem with result from g_rdf

Dear all, When I use g_rdf to find the rdf between the alpha C-atoms in my simulation, I get the usually expected result.However, when I use g_rdf to get the rdf between just the central alpha C-atoms of the two peptides (my simulation is 2 peptide in a box of water, each peptide has 3 residues