Re: [gmx-users] Parametrisation of the heteroatomic pdb

Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? What difference beetwen different caps I cant unde

Re: [gmx-users] Parametrisation of the heteroatomic pdb

On 10/11/2011 7:05 PM, James Starlight wrote: Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function?

Re: [gmx-users] Normal Mode Analysis

Hi James, PCA on a trajectory is about fluctuations -the correlation between deviations from an average positions-, NMA is about penalized displacement -the increase in potential energy due to concurrent displacement-. In NMA the lowest mode is that for which most atoms can move most unrestrictedl

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Thanks Mark, 1) By the way do you know any database where I could obtain information about function of the specific CAP groups ? E.g as I know the most spread CAP on N is ACE group but in my case there is For ( simple COH group) instead of ACE. I think that parametrisation of such simple groups s

Re: [gmx-users] orca question and LA

Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubs

Re: [gmx-users] Parametrisation of the heteroatomic pdb

On 10/11/2011 7:36 PM, James Starlight wrote: Thanks Mark, 1) By the way do you know any database where I could obtain information about function of the specific CAP groups ? E.g as I know the most spread CAP on N is ACE group but in my case there is For ( simple COH group) instead of ACE. I

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

Dear Xi Zhao, The ORCAINFO file is no tok. You should not give the Opt keyword there. GMX is taking care of the optimization. If you provide the Opt keyword, ORCA will do an optimization in each QM forces calculation, but neglecting the QM-MM interactions, and this is not what you want. So k

[gmx-users] Disulphur bridge parameters

Dear gromacs users, I am simulating a protein complex with a disulphur bridge. I put the two chains in the same "moleculetype" definition, and through pdb2gmx I generate the disulfur bridge. When I checked the .top file for angles and dihedral angles potential parameters I found out that these fiel

[gmx-users] Converting of itp topology files

Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existing .itp topology? Thanks, James -- gmx-users m

Re: [gmx-users] CygWin and Gromacs 4.5.5

yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks From: Roland Schulz To: Discussion list for GROMACS users Sent: Wednesday, November 9, 2011 11:03 AM Subject: Re: [gmx-users] CygWin and Gromacs 4.5.

[gmx-users] what's the meaning of g_msd's -trestart

dear teacher, i read the groace_manual-4.5.4: i found "The time between the reference points for the MSD calculation is set with -trestart." and "the defaut is 10ps." do it computer the "msd" like this : 0ns compared with "-beginfit to -endfit " 10ns compared with "-beginfit to -endfit " 20ns compa

Re: [gmx-users] Running QM/MM in parallel (ORCA/GMX)

Dear Micha, I just saw your mail and perhaps it got already solved in the past. Otherwise: First you should try to set up ORCA calculations in parallel. If that is working, it is relatively straightforward for ORCA/GMX. Simply start GMX one a single CPU, and let ORCA run on several CPUs (by ad

Re: [gmx-users] orca question and LA

I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi   then make   make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze 写道： 发件人: Micha Ben Achim Kunze 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10

Re: [gmx-users] orca question and LA

I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html www.google.com etc. For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in parallel yet (using c

Re: [gmx-users] Converting of itp topology files

On 10/11/2011 9:30 PM, James Starlight wrote: Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existin

Re: [gmx-users] Disulphur bridge parameters

On 10/11/2011 9:28 PM, alberto arrigoni wrote: Dear gromacs users, I am simulating a protein complex with a disulphur bridge. I put the two chains in the same "moleculetype" definition, pdb2gmx does not read [moleculetype] definitions, it writes them. and through pdb2gmx I generate the disul

Re: [gmx-users] Converting of itp topology files

Mark, The problem is that my .itp done for old gromos ff consist of parameters for molecule wich has some specific groups wich not preset in the gromos96 ff so pdb2gmx is not good decision :) By the way I'm intresting what changes were done in the dihedrail terms since gromos87 ff. E.g I found t

Re: [gmx-users] Converting of itp topology files

On 10/11/2011 10:43 PM, James Starlight wrote: Mark, The problem is that my .itp done for old gromos ff consist of parameters for molecule wich has some specific groups wich not preset in the gromos96 ff so pdb2gmx is not good decision :) Then you'll have to work out how the old .itp worked

Re: [gmx-users] Running QM/MM in parallel (ORCA/GMX)

Hey Christoph, I got orca and gmx working in parallel and I already tried it the way you mentioned with gmx on a single cpu and orca with !PALX in the past (with combinations of gmx compiled w/ and w/o mpi enabled), which did not seem to work. I will give it another go! Thanks, Micha On 10/1

Re: [gmx-users] about the velocity output from leap-frog integrators

On 9/11/2011 9:44 PM, Ravi Bhadauria wrote: Hello users, I have few conflicting answers from the user mailing list about the following question. Using leap-frog integrator, what is the velocity that is WRITTEN in the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2) or v(t). Ha

[gmx-users] Problems with g_membed tools

Hello all, I want to use g_membed to insert a protein in POPC. I followed the manual steps. I used the grompp to generate the tpr file. It works well. But when I handed this tpr file to g_membed, it returned this: --- Program g_membed, VERSION

Re: [gmx-users] what's the meaning of g_msd's -trestart

杜波 wrote: dear teacher, i read the groace_manual-4.5.4: i found "The time between the reference points for the MSD calculation is set with -trestart." and "the defaut is 10ps." do it computer the "msd" like this : 0ns compared with "-beginfit to -endfit " 10ns compared with "-beginfit to -end

Re: [gmx-users] Problems with g_membed tools

On 11/11/2011 12:05 AM, LindaSong wrote: Hello all, I want to use g_membed to insert a protein in POPC. I followed the manual steps. I used the grompp to generate the tpr file. It works well. But when I handed this tpr file to g_membed, it returned this: --

[gmx-users] gromacs/mopac compilation: linking libmopac

Hi all I am trying to compile gromacs with mopac but I'm experience some problems using libmopac.a. I have a x86_64 processor and I'm trying with gromacs-4.5.5. I've followed the instructions at the website (i.e. to compile libmopac.a, I've used the alternte dcart.f and gmxmop.f) but I didn't

Re: [gmx-users] CygWin and Gromacs 4.5.5

On Tue, Nov 8, 2011 at 11:59 PM, Mark Abraham wrote: > On 8/11/2011 11:35 PM, Szilárd Páll wrote: > >> Hi, >> >> There have been quite some discussion on the topic of GROMACS on >> Cygwin so please search the mailing list for information. >> > > Actually I don't think this issue has been addressed

Re: [gmx-users] CygWin and Gromacs 4.5.5

On Thu, Nov 10, 2011 at 5:37 AM, Mr Bernard Ramos wrote: > yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I > hope this issue will be addressed.Thanks > The slow IO performance under cygwin is a known problem with the approach of cygwin and happens with any cygwin program and

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACB

Re: [gmx-users] Parametrisation of the heteroatomic pdb

On 11/11/2011 3:01 AM, James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Cheers Tom James Starlight wrote: Mark, I've mistaken I need to i

Re: [gmx-users] Parametrisation of the heteroatomic pdb

On 11/11/2011 3:17 AM, Thomas Piggot wrote: Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Good thought :-) I finall

[gmx-users] Re: sudden drop of minimal periodic distance

t was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2010/7b9ed4a5/attachment-0001.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: [gmx-users] Re: sudden drop of minimal periodic distance

--- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2010/7b9ed4a5/attachment-0001.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Thomas, thank you! It's my inattention so I've missed DALA in the rtp file :( So as I've understood the difference just in one string CA N CCB gi_2 for L form CB N CCA gi_2 for D form :D James 2011/11/10 Thomas Piggot > Hi James, > > I suggest to see the d

[gmx-users] Re: Problems with g_membed tools

Thank you for reply. I am sorry I didn't apply more information There are only protein and lipids in my system now. I used the CHARMM ff. The topology is like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC1 In the grompp step, I u

Re: [gmx-users] Re: Problems with g_membed tools

On 11/11/11, LindaSong wrote: > Thank you for reply. I am sorry I didn't apply more information > > There are only protein and lipids in my system now. I used the CHARMM ff. The > topology is like this: > [ molecules ] > ; Compound#mols > Protein_chain_A 1 > Protein_chain_A2

Re: [gmx-users] about the velocity output from leap-frog integrators

Thank you for your answer Mark. I was not able to find this information in manual. If it is present, could you please refer me to the relevant section. If it is indeed not there, it would be very helpful to include it in the manual. Sincerely, Ravi Bhadauria On Thu, Nov 10, 2011 at 6:18 AM, Mar

[gmx-users] Positive potential energy for TFE solvent

Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: >> editconf -f

Re: [gmx-users] Re: Problems with g_membed tools

Thank you very much for your reply, Mark It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC 256 This problem s

Re: [gmx-users] Re: Problems with g_membed tools

On 11/11/2011 5:13 PM, LindaSong wrote: Thank you very much for your reply, Mark It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POP

[gmx-users] Insertion of the protein into membrane with Gmembed

Dear Gromacs Users! I have some questions about insertion protein into membrane with Gmembed 1) I've used default parameters from gmembed manual for preparing input for insertion integrator = md energygrp = Protein freezegrps = Protein freezedim = Y Y Y energygrp_table energy

[gmx-users] Re: mdp file problem

Dear Justin, I could solve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds. On Thu, Nov 10, 2011 at 7:28 PM, madhumita das wrote: > Dear