Re: [gmx-users] Error in BlueGene

Hello Cíntia, On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote: Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by I balance the domain decomposition for the

[gmx-users] Unusual g_order with CHARMM36

Dear Gmx users, anyone which used the CHARMM36 (available for downloading in the Gromacs website) for simulating a POPC, POPE or whatever POxx membrane in Gromacs has found an unusual behavior in the Oleyl chain when it comes to the deuterium order parameter (Scd)? Let me explain a little

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

I thank you all so much for aiding me on this matter, Jan, Peter and Justin. Now things are way clerarer! Cheers, Ricardo. De: Peter C. Lai p...@uab.edu Para: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Sábado, 19 de

[gmx-users] Different Lipids into one Moleculetype (for position restrain)

would I have should I set both POPC and POPE to Lipid, however in different itp files. Does anyone know a more elegant solution? Thanks Ricardo. ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences

Re: [gmx-users] NBFIX to gromacs

Dear Mr. Lai, I see. I'll look more deeply into it, thanks for your answer. Ricardo.   De: Peter C. Lai p...@uab.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quarta-feira, 2 de

Re: [gmx-users] NBFIX to gromacs

pair. On 2012-04-30 01:30:59PM -0700, Ricardo O. S. Soares wrote: Hello GMX users, does anyone that dealt with Charmm before knows how to translate the NBFIX section into a Gromacs ff format? After convertion from KCal to KJ, does it go into [pairtypes]? I see that it concerns

[gmx-users] NBFIX to gromacs

Hello GMX users, does anyone that dealt with Charmm before knows how to translate the NBFIX section into a Gromacs ff format? After convertion from KCal to KJ, does it go into [pairtypes]? I see that it concerns to corrections in LJ interactions, however the charmm documentation seems a bit

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

to calculate absent 1-4 interactions in CHARMM36c FF On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Oh, I see. I did inserted only the provided values from CHARMM ff prm file. Now I'll do some testing... Thanks Peter, ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São

[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two

[gmx-users] Charmm Cholesterol parameters - str to itp

. Chem. Soc., 2012, DOI: 10.1021/ja211929h) are providing cholesterol .itp for OPLS-AA. Could that maybe be a different starting point? Thanks for eventual reply, Ricardo.   ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty

Re: [gmx-users] Charmm Cholesterol parameters - str to itp

you David, that is really helpful!  I'll give it a try! Cheers Ricardo. --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP

[gmx-users] genconf -renumber merges atom number and ID columns

could write a post-processing script to add the spaces, but I'm curious about this issue. Any help is appreciated, Thanks! Ricardo.   ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto

Re: [gmx-users] genconf -renumber merges atom number and ID columns

. De: Justin A. Lemkul jalem...@vt.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quinta-feira, 1 de Março de 2012 16:07 Assunto: Re: [gmx-users] genconf -renumber merges atom number and ID columns Ricardo O. S. Soares

[gmx-users] Peptide protonation inside membrane

Dear Users, when using pdb2gmx with the -inter flag, how should one manage the residues charges of a peptide which is fully embedded in a lipid bilayer? It seems that there are evidences that ARG residue remains protonated inside the membrane

Re: [gmx-users] Peptide protonation inside membrane

Hi Justin, thanks, for your reply. I'm going to check H++ tools on my system. Cheers,   ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo

[gmx-users] how to create a proper box size for a membrane?

there yet. Thanks   ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] how to create a proper box size for a membrane?

and edit its size? Don't know if its relevant here, but I intend to use Charmm27. Thanks again, Ricardo.   De: Tsjerk Wassenaar tsje...@gmail.com Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas

[gmx-users] Spherical Position Restrain from the center of the Box

file. Is there a way to include this whole selection into the top file directly? Where/how could that be? I've searched for solutions for a while, with no avail. Thanks,   ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty

Res: [gmx-users] different number of waters (grompp)

Ricardo O. S. Soares wrote: Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error

[gmx-users] different number of waters (grompp)

Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error: --- Program

[gmx-users] V-Rescale Reference

Dear users, what is the literature reference for using the V-Rescale Thermostat? Maybe the Gromacs 4 paper? Thank you --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University

Res: [gmx-users] V-Rescale Reference

Ok, thanks Erik. De: Erik Marklund er...@xray.bmc.uu.se Para: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Ricardo O. S. Soares ross_...@yahoo.com.br Enviadas: Quinta-feira, 3 de Março de 2011 18:58:30 Assunto: Re: [gmx-users] V-Rescale

Res: [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

separately. Thank you Lin Ricardo. --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil

[gmx-users] 5 identical simulations -- 5 different results, why?

does anyone have a clue at which step is it possible that those little differences are being brought into the systems? I'm guessing the grompp step... Thanks a lot. --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical

[gmx-users] No Temperature Coupling to protein

of the coupling group. Is there a way to do that in gromacs? Thanks. --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903

[gmx-users] Re: No Temperature Coupling to protein (Justin A. Lemkul)

Oh yes I see, thanks Justin! Ricardo O. S. Soares wrote: Hi gmx users, I'd like to run a test simulation, in which the temperature coupling is not on for the protein, yet active for the solvent and ions. If I specify in the tc-grps only Non-protein

[gmx-users] Segmentation fault (11)

*** Segmentation fault Any ideas? Thank you. --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil

[gmx-users] SHAKE and LINCS

Hello everyone, which one is used by default in case I do not provide any of them in the mdp file for molecular dynamics? Thanks! --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto

[gmx-users] mpirun.gromacs errors

symbol: orted_cmd_line The command mdrun -s pr.tpr -v if fine, though it uses only one node... Thanks a lot for any clarification! Ricardo. --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão