[gmx-users] multiple outputs in mdrun with gromacs-4.0.3

Hi There, I have upgraded my Gromacs version from 3.3 to 4.0.3. I am using it with mpi over 24 processor and 3 nodes (each node having 8 processor). I fired an energy minimization run. while doing do, I found multiple copies of output files (.edr, .gro, .trr) instead of single file. Following is

Re: [gmx-users] multiple outputs in mdrun with gromacs-4.0.3

vivek sharma wrote: Hi There, I have upgraded my Gromacs version from 3.3 to 4.0.3. I am using it with mpi over 24 processor and 3 nodes (each node having 8 processor). I fired an energy minimization run. while doing do, I found multiple copies of output files (.edr, .gro, .trr) instead of

RE: [gmx-users] grompp 4.0.5 hangs while 3.2.1 works

Hi, You have an error in your input file. Does grompp also hang with correct mdp parameters? Berk Date: Thu, 21 May 2009 23:55:32 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] grompp 4.0.5 hangs while 3.2.1 works Kaihsu Tai wrote: I have a system

[gmx-users] wrong number of control atoms (3 iso 4) on line

Dear all, I am trying to do simulation of DNA-protein complex . For this purpose I am using ffoplsaano force field which is already charged with ffamber force field which I have got from golovin_at_genebee.msu.su website . I am using this force field with pdb2gmx

[gmx-users] problem with system neutralization

Dear all, As the on-screen output of grompp says, my system has non-zero total charge = -4.000 Thus, I'm trying to neutralize the system using genion with this command line: genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -neutral The problem is that the on-screen

Re: [gmx-users] problem with system neutralization

Hello, Greetings from Pawan. -np is a parameter used to add the nmber of positive ions. when u have -4 negative charge u should give -np 4. -np with -pname will be more appropriate. see through this website for the proper usage of genion options.

[gmx-users] Re: grompp 4.0.5 hangs while 3.2.1 works

It seems that there was some change in reading the fields ‘cpp’, ‘include’, and ‘define’ from the .mdp file. Now I have set the GMXLIB environment variable rather than relying on those .mdp fields and it seems to work. Cheers. Kaihsu Tai, 2009-05-21 16:07:03+0100: I have a system which works

Re: [gmx-users] problem with system neutralization

Thanks Pawan, I added 4 positive ions as you suggested but the system total charge reported in genion.log is still -4! Why? Cheers, Stefano Pawan Kumar ha scritto: Hello, Greetings from Pawan. -np is a parameter used to add the nmber of positive ions. when u have -4 negative charge u

Re: [gmx-users] in vacuo minimization of a multimeric protein

Dear Justin, thank you very much for suggestion. Now it works! Anna Message: 4 Date: Thu, 21 May 2009 10:39:33 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] in vacuo minimization of a multimeric protein To: Discussion list for GROMACS users gmx-users@gromacs.org

Re: [gmx-users] problem with system neutralization

Hello, Greetings from Pawan. Giving the command and the options being used will be much better to give any further probable suggestions. Just using -np 4 wont solve the problem as such. You should specify the -pname option also. You can use NA+ ions to neutralize the system as its having

[gmx-users] simulation of protein in popc box

hi i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably POPC or POPE). i have generated the protein inside the POPC box complex. But whenever i am going to build the .gro and .top file of that complex with pdb2gmx an error is creeping in saying Cant find POP in

Re: [gmx-users] simulation of protein in popc box

Hello, Greetings from Pawan. Topologies for lipids like POP are not available in the topology database in gromacs. So the starting point would be to generate a topology and a gro file for the protein alone as such and then edit the topology to include the .itp files as specifically needed for the

[gmx-users] changelog for gmx 4.0.5?

Hi There, Where can I find a summary of the modifications and news about gmx 4.0.5? Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28

Re: [gmx-users] mdp file to calculate local pressure

anirban polley wrote: Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by

Re: [gmx-users] wrong number of control atoms (3 iso 4) on line

nitu sharma wrote: Dear all, I am trying to do simulation of DNA-protein complex . For this purpose I am using ffoplsaano force field which is already charged with ffamber force field which I have got from golovin_at_genebee.msu.su

Re: [gmx-users] problem with system neutralization

As an aside, I have found that using the -neutral flag of genion only works in conjunction with a specified -conc. This is somewhat counterintuitive and not explained by the documentation. Is this perhaps a bug? -Justin Pawan Kumar wrote: Hello, Greetings from Pawan. Giving the command

Re: [gmx-users] simulation of protein in popc box

Samik Bhattacharya wrote: hi i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably POPC or POPE). i have generated the protein inside the POPC box complex. But whenever i am going to build the .gro and .top file of that complex with pdb2gmx an error is creeping in

Re: [gmx-users] simulation of protein in popc box

Thanks pawan, for helping but one problem still remains that is how to incorporate the .itp file inside the topology file and which .itp file should i include is it the lipid.itp orr POPC.itp?? thanx for your help Shamik Greetings from Pawan. Topologies for lipids like POP are not

Re: [gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer

nitu sharma wrote: Dear all I am running keepbyz.pl script to remove unwanted waters from hydrophobic core of lipid . I am getting problem in this process. For this I follow the chris neale rule - /1. run genbox on initial.gro to create solvated.gro // 2. cp

Re: [gmx-users] changelog for gmx 4.0.5?

Alan wrote: Hi There, Where can I find a summary of the modifications and news about gmx 4.0.5? Alan http://www.gromacs.org/content/view/181/132/ -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124

Re: [gmx-users] simulation of protein in popc box

Hello Shamik, Going through the membrane protein tutorial will help you to get answers to these questions. The lipid.itp file has to be modified and edited depending on the force fields being used like opls force field or the gromos96 force field. Popc.itp file should also be included in order to

[gmx-users] question about positive potential

Hi all, After a 3ns MD run, I took a look at the  .log file, and found the potential is positive. How could it be?!  I wonder what is the problem.  The standard deviation of density is small, while the SD of potential is big. Is the system not equilibrated (if yes, why the sd of density is so

RE: [gmx-users] bond, angle and dihedral restraints in Gromacs

Thank you very much for the suggestion. Actually, I am trying to reproduce the results from another publication (JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d where they used Gromacs/amber to simulate a CNT. They apply: Carbon−carbon bond lengths of 0.14 nm and bond

Re: [gmx-users] bond, angle and dihedral restraints in Gromacs

Rebeca García Fandiño wrote: Thank you very much for the suggestion. Actually, I am trying to reproduce the results from another publication (JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d where they used Gromacs/amber to simulate a CNT. They apply: Carbon−carbon bond

Re: [gmx-users] bond, angle and dihedral restraints in Gromacs

Rebeca García Fandiño wrote: Thank you very much for the suggestion. Actually, I am trying to reproduce the results from another publication (JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d where they used Gromacs/amber to simulate a CNT. They apply: Carbon−carbon bond

Re: [gmx-users] question about positive potential

Baofu Qiao wrote: Hi all, After a 3ns MD run, I took a look at the .log file, and found the potential is positive. How could it be?! I wonder what is the problem. The standard deviation of density is small, while the SD of potential is big. Is the system not equilibrated (if yes, why the

Re: [gmx-users] problem with system neutralization

Hi again, Apologies for my last imprecise email. Using the command $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb genion.log still reports: System total charge: -4.000 Stefano 2009/5/22, Pawan Kumar

Re: [gmx-users] problem with system neutralization

Stefano Meliga wrote: Hi again, Apologies for my last imprecise email. Using the command $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb genion.log still reports: System total charge: -4.000 The logfile should report

Re: [gmx-users] question about positive potential

Hi Mark, There are two polyelectrolytes in my systems: poly(sodium 4-styrenesulfonate) and poly(diallyl dimethyl ammonium chloride). And Actually sodium and chloride are absent, only the polycation and the polyanion. I didn't find suitable force field for sulfonate, thus I used the reported force

Re: [gmx-users] question about positive potential

Baofu Qiao wrote: Hi Mark, There are two polyelectrolytes in my systems: poly(sodium 4-styrenesulfonate) and poly(diallyl dimethyl ammonium chloride). And Actually sodium and chloride are absent, only the polycation and the polyanion. I didn't find suitable force field for sulfonate, thus I

[gmx-users] What is the purpose that we make the bond constraints?

Hi All atoms are connected by the covalent bonds and all atoms are constrainted by the force field. Why do we need the bond constraints? What is the purpose that we make the bond constraints? I read the manual but could not answer the question by myself. How do the following parameters work? ;

Re: [gmx-users] What is the purpose that we make the bond constraints?

Chih-Ying Lin wrote: Hi All atoms are connected by the covalent bonds and all atoms are constrainted by the force field. Why do we need the bond constraints? chapter 1. What is the purpose that we make the bond constraints? I read the manual but could not answer the question by myself.

Re: [gmx-users] What is the purpose that we make the bond constraints?

Chih-Ying Lin wrote: Hi All atoms are connected by the covalent bonds and all atoms are constrainted by the force field. Why do we need the bond constraints? What is the purpose that we make the bond constraints? I read the manual but could not answer the question by myself. References 33

Re: [gmx-users] extending simulations

Hello, I am having a similar issue. When using Gromacs version 4.0.4 and running mdrun with the -append flag on a traj.trr file over 2GB I get an error stating Truncation of traj.trr file failed. However, when I use version 4.0.2 it seems to append fine even with very large files. Any ideas as to

[gmx-users] Why does protein carry charges?

Hi I got the protein crystal structures from the PDB file. There are only residues and water in the PDB files. Why does the protein carry charges? Why aren't they electrically neutral? What are their intrinsic counter ions ? Thank you Lin ___

Re: [gmx-users] Why does protein carry charges?

Hi Lin, It sounds like you need to look at a basic chemistry or biochemistry textbook. The protein itself in the PDB shouldn't carry a charge explicitly until you decide on the pH of your system and assign the protonation/deprotonation state of residues and add hydrogen atoms appropriately. While

[gmx-users] How to choose the counter ions for proteins?

Hi How to choose the counter ions for proteins? Proteins are made of amino acids. Does it mean the counter ions of protein H+ or OH-? I think = H+ and OH- ions are not available for the gromos force field, right? But, later version 4.0.2 ; they might be available, right? Thank you Lin