[gmx-users] Re: CHARMM36 force field available for GROMACS
Hello Justin, Two quick questions, here - Since the lipid charmm36 parameters for lipids are already available in the gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas Piggot. Does it means that these files are considered as deprecated and all the users are invited to use in their simulations the CHARMM -GROMACS official release from you ? - Did you compare the results for the common molecules, to see if some errors/typos in charmm36.ff_4.5.4_ref.tgz were presents ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE : gmx-users Digest, Vol 114, Issue 21
OK thank you four kind response. And also thank you and the CHARMM team for this geat job. Stephane --- On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote: Hello Justin, Two quick questions, here - Since the lipid charmm36 parameters for lipids are already available in the gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas Piggot. Does it means that these files are considered as deprecated and all the users are invited to use in their simulations the CHARMM -GROMACS official release from you ? AFAIK, the charmm36.ff_4.5.4_ref.tgz only contains updated CHARMM36 lipids and nothing else. Someone please correct me if I am wrong here, but a quick scan through that archive indicated to me that the force fields for other molecules (proteins, nucleic acids, etc) were outdated. Thus, I feel that our new distribution supersedes the available files because what is contained there is not what we consider the CHARMM36 force field in its entirety. Users are welcome to use whatever they like, but our distribution is the only one (to our knowledge) that is equivalent to the current force field set distributed with CHARMM and does contain an important reparametrization of the CMAP terms that go along with what we call the CHARMM36 protein force field, which is probably of particular interest to this community. - Did you compare the results for the common molecules, to see if some errors/typos in charmm36.ff_4.5.4_ref.tgz were presents ? We did not look into any errors or typos in other distributions. We created our files completely on our own directly from existing CHARMM force field files, not based on anything found in charmm36.ff_4.5.4_ref.tgz. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] script to convert the TIP3P water model into TIP4P
Hello all, It is not a gromacs problem per se, but I hope that some gromacs users can help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005 water model. I have downloaded in the Klauda's website several bilayer starting conformations. However, since CHARMM uses the TIP3 water model, I am confused to convert the water coordinates into a water four sites. Does somebody has a little script to share with me that can help me? Thank you for kindly help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] script to convert the TIP3P water model into TIP4
Hello, Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model. Stephane -- Message: 8 Date: Mon, 23 Sep 2013 10:45:56 +0200 From: Dr. Vitaly Chaban vvcha...@gmail.com Subject: Re: [gmx-users] script to convert the TIP3P water model into TIP4P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: capxdd+alyfc4g+wnzj7bk0+rj3eexj_js7stjtdwymayt5t...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 I am confused. Why do you want 4-sites water? Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, It is not a gromacs problem per se, but I hope that some gromacs users can help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005 water model. I have downloaded in the Klauda's website several bilayer starting conformations. However, since CHARMM uses the TIP3 water model, I am confused to convert the water coordinates into a water four sites. Does somebody has a little script to share with me that can help me? Thank you for kindly help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ***-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] script to convert the TIP3P water model into TIP4(P)/2005
Hello Justin, Thank you for your response and your interest for my simulations ;) I am of course aware that the primary water model for the CHARMM is the TIP3(S)P model. Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]). [1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/ [2] Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550–1560. Stephane On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote: Hello, Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model. The math for producing the virtual site in TIP4P is described in tip4p.itp, so you can use that. What's more curious is that if a paper claims to use TIP4P but the provided files use TIP3P, then either there has been a mix-up in the files or an error in the paper. In either case, I find it odd to use TIP4P with CHARMM, especially given the sensitivity of lipid parameters to the water model. Without knowing the paper you're talking about, I will not criticize the choice as it may have been justified. It's probably a good question to ask of the corresponding author of the study you are trying to reproduce. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE : gmx-users Digest, Vol 113, Issue 106
Finally, I have resolved my (little) problem: I used CHARMM-GUI to constructed the membrane, removed the TIP3 water molecules and then resolvate the bilayer with TIP4P/2005 water molecules. The simulation seems to work. Stephane On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote: Hello Justin, Thank you for your response and your interest for my simulations ;) I am of course aware that the primary water model for the CHARMM is the TIP3(S)P model. Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]). [1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/ [2] Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550?1560. It sounds like you're on the right track, at least knowing that a considerable amount of work has to be done to prove that the force field + water model combination is sound. Given that you're going to have to re-equilibrate the water anyway, I don't see why you have to start with TIP3P and try to hack it into becoming TIP4P; I would just strip the water and re-solvate. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Select atoms in a residue
Hello all, A Quick question below: My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files The atom name in the indol group are aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1 Can you help me ? Best, Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Select atoms in a residue
Hello Justin, My question was How to select the following atoms CG, CD1, HD1, CD2, CE3, HE3, CZ3, HZ3, CH2, etc.. present ONLY in the trp residue with a single line command with make_ndx. Indeed some of them can be also present in other residues. Stephane -- Message: 4 Date: Tue, 3 Sep 2013 12:57:25 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Select atoms in a residue To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a880...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii Hello all, A Quick question below: My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files The atom name in the indol group are aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1 Can you help me ? Best, Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How do I make an AOT reverse micelle, which package I should use
Hello, I have a done a lot of simulations of reverse micelles. For me to construct the best model of preformed RM you can indeed use Packmol. But after that, you will carry out out different equilibration stages to obtain stable reverse micelles. I want to arrange charge, LJ parameter, hydrogen bond length? protonation state of the water molecules, and the proper orientation like angles as well. About what ? Sorry I do not not understand your questions. Moreover, since you will do classical MD, water state will not change at all during the simulation Stéphane -- Message: 5 Date: Fri, 12 Jul 2013 18:36:03 -0700 (PDT) From: Hari Pandey hariche...@yahoo.com Subject: [gmx-users] How do I make an AOT reverse micell, which package I should use To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1373679363.26833.yahoomail...@web163003.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi all GROMACS users, I need to make a pdb file of AOT reverse micell . Please some body tell me how do I build it and which package would best for this work. Now I am using PACKMOL but it seems just a geometrical mathematical manipulation. I want to arrange charge, LJ parameter, hydrogen bond length? protonation state of the water molecules, and the proper orientation like angles as well. I don't know how do I use all these parameters in PACKMOL. So please advice me which package could be good for this purpose. I appreciate your help. Thank you very much Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] probability from COM of micelle
Hi, You indeed could use the g_rdf command like this (in the script) g_rdf_mpi -f $pathXTC -s $pathTPR -n bOG_Micelle_RDF.ndx -norm -com -b $timeBegin1 -e $timeEnd1 -o $name1_$name2_$name3_$i_original.xvg RadDensFunc_$i.txt Where in the RadDensFunc.txt file, i choose as the first group the micelle group (for the micelle COM) and as the second group the micelle atom you want to plot the rdf (i.e. surfactant headgroup, alkyl tail, etc?) Do not forget to take into account the (average) volume of the simulation cell and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in nm-1) HTH On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 2 Date: Thu, 09 May 2013 21:03:44 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Fw: probability from COM of micelle To: gmx-users@gromacs.org Message-ID: 518bf310.6020...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2013-05-09 20:15, Justin Lemkul wrote: On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin How about g_rdf? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Message: 3 Date: Thu, 9 May 2013 13:33:54 -0700 From: Eric Stokes es...@uw.edu Subject: [gmx-users] Charmm27 potential energies. To: gmx-users@gromacs.org Message-ID: capsvvmtorup3gnxthy6gkouevenstp1qydhgr7yweq-r8vg...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hello, I am attempting to generate force-field parameters for a fatty acid molecule that contains a carboxilic acid head group. I decided to use the parameters for stearic acid as the base for my molecule, since they contain similar structures with the only major change being a shorter hydrophobic tail. I noticed that the charge on stearic acid, and other molecules that have a carboxilic head group, is spread out with -0.9 residing on the head group and -0.1 on the second carbon. I need to use the protonated from of my molecule for my simulation, as well as the deprotonated form. I looked into the parameters for the COOH replacement in the Charmm27 force-field and used that to form the head group of the protonated form of my molecule. The problem that I am facing is that this left behind a charge of -0.1 that resides on the second carbon. Is there any way to find acceptable partial charges without doing the full Gaussian calculations? I would also appreciate it if someone could explain why the charges were split onto the second carbon in the first place. Thanks in advance, Eric Stokes -- Message: 4 Date: Thu, 09 May 2013 16:39:41 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Charmm27 potential energies. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 518c098d.2080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/9/13 4:33 PM, Eric Stokes wrote: Hello, I am attempting to generate force-field parameters for a fatty acid
[gmx-users] RE: Martini with PME, temp two low
Hi Xavier, I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system. Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Martini with PME, temp two low
Xavier, as i said in my message, this nstlist value is not optimal, but it works !!! if wlll try a higher nstlist value, if I have same problem in futur simulations Thanks again for you help Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Martini with PME, temp two low
Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 8.02685e+04 -2.3e+052.98129e+02 -3.07123e+01 Box-X Box-Y Box-Z 1.52926e+011.52926e+011.52926e+01 T-AOT_W_ION T-OCT 2.98141e+022.98129e+02 Did I miss something ? Note that for the moment i do not use the polarizable water model. Thanks for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE : gmx-users Digest, Vol 108, Issue 154
Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- Message: 5 Date: Thu, 25 Apr 2013 13:34:21 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl Content-Type: text/plain; charset=us-ascii Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 8.02685e+04 -2.3e+052.98129e+02 -3.07123e+01 Box-X Box-Y Box-Z 1.52926e+011.52926e+011.52926e+01 T-AOT_W_ION T-OCT 2.98141e+022.98129e+02 Did I miss something ? Note that for the moment i do not use the polarizable water model. Thanks for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Message: 6 Date: Thu, 25 Apr 2013 14:05:51 +0200 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID
Re: [gmx-users] Martini with PME, temp two low
Sorry for the double post, but i forgot to remove the others message. I have also added the average values obtained for this run Statistics over 20001 steps using 4001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.65683e+041.26644e+03 -4.02287e+05 -8.47260e+03 -4.90494e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41974e+057.91982e+04 -3.62776e+052.94154e+02 -1.80237e+01 Box-X Box-Y Box-Z 1.51316e+011.51316e+011.51316e+01 Total Virial (kJ/mol) 2.90936e+04 -4.68005e+01 -2.46005e+01 -4.68005e+012.92687e+04 -2.56235e+01 -2.46006e+01 -2.56236e+012.64822e+04 Pressure (bar) -2.57341e+015.58858e-011.46893e-01 5.58858e-01 -2.74443e+012.21040e-01 1.46893e-012.21041e-01 -8.92609e-01 Total Dipole (D) 4.16699e+021.92049e+026.43137e+02 Epot (kJ/mol)Coul-SR LJ-SR AOT-AOT5.26697e+02 -4.94208e+03 AOT-W0.0e+00 -2.35002e+03 AOT-ION -9.54002e+03 -1.89339e+03 AOT-OCT0.0e+00 -2.04448e+04 W-W0.0e+00 -3.88078e+02 Stephane -- Message: 4 Date: Thu, 25 Apr 2013 13:26:32 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] RE : gmx-users Digest, Vol 108, Issue 154 To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- Message: 5 Date: Thu, 25 Apr 2013 13:34:21 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl Content-Type: text/plain; charset=us-ascii Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames
[gmx-users] Martini with PME, temp two low
And ? sorry but i do not understand... Stephane -- Message: 2 Date: Thu, 25 Apr 2013 15:39:12 +0200 From: Dr. Vitaly Chaban vvcha...@gmail.com Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAPXdD+bDiuQWG_3eWZ_0yb=aynlaaf08vt46usel4wk_bjg...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hmmm Aren't the keywords here charged system + PME? Dr. Vitaly Chaban On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote: Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 8.02685e+04 -2.3e+052.98129e+02 -3.07123e+01 Box-X Box-Y Box-Z 1.52926e+011.52926e+011.52926e+01 T-AOT_W_ION T-OCT 2.98141e+022.98129e+02 Did I miss something ? Note that for the moment i do not use the polarizable water model. Thanks for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Martini with PME, temp two low
@ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- Message: 5 Date: Thu, 25 Apr 2013 13:34:21 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl Content-Type: text/plain; charset=us-ascii Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature
[gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)
Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GROMOS54A8 parameters in GROMACS format
Hello, Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case for the AA topology where several changes were done. So any help will be appreciate.. Stephane -- Message: 5 Date: Thu, 14 Feb 2013 11:18:17 +0100 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20130214101817.72...@gmx.net Content-Type: text/plain; charset=utf-8 Dear Stephane Abel, Theres a link I on the gromacs web site to ATB, or you can google it. If it is not in Gromacs format you can just write a couple 6 liner scripts to re-format it by parsing into the gromacs format, Stephan Watkins Original-Nachricht Datum: Wed, 13 Feb 2013 21:25:33 + Von: ABEL Stephane 175950 stephane.a...@cea.fr An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247???1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 106, Issue 73 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GROMOS54A8 parameters in GROMACS format
Thanks Berk, I have found the script, I will try them Best Stephane Message: 4 Date: Thu, 14 Feb 2013 13:53:56 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: dub124-w200b8c2eb085c78933a9418e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, There are two scripts make_gromos_rtp in the scripts directory which were used to convert Gromos AA topologies to rtp entries. Cheers, Berk From: stephane.a...@cea.fr To: gmx-users@gromacs.org Date: Thu, 14 Feb 2013 11:34:59 + Subject: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format Hello, Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case for the AA topology where several changes were done. So any help will be appreciate.. Stephane -- Message: 5 Date: Thu, 14 Feb 2013 11:18:17 +0100 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20130214101817.72...@gmx.net Content-Type: text/plain; charset=utf-8 Dear Stephane Abel, Theres a link I on the gromacs web site to ATB, or you can google it. If it is not in Gromacs format you can just write a couple 6 liner scripts to re-format it by parsing into the gromacs format, Stephan Watkins Original-Nachricht Datum: Wed, 13 Feb 2013 21:25:33 + Von: ABEL Stephane 175950 stephane.a...@cea.fr An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247???1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 106, Issue 73 ** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Message: 5 Date: Thu, 14 Feb 2013 08:01:43 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] different springs - WHAM To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 511ce037.5020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/13/13 5:23 PM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:57 AM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to combine windows with different spring constants into the one PMF curve using g_wham. Do I have to somehow tell g_wham that one or two windows have different spring constants? No, they are read from the .tpr files. For instance - I got the better histogram overlap with lower force constant in one window. When I replace this window into the window with the sring constant like all windwos (worse overlap) both PMF curves differ app. 2kcal/mol which is around 30% of the overall deltaG. Is there any error I should inroduce when one window differ in terms of k1? What does g_wham's error analysis suggest? -Justin In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol Seems like a good result, so what's the problem? -Justin That the better overlap of histograms produce worse deltaG comparing to experiment. With all the same spring constants I get the experimental value of deltaG but there is a poor overlap. There must be (somehow) a correction added to deltaG when introdcuing windows with different spring constants. The code and/or g_wham paper should address this. In principle, WHAM can be conducted with any assortment of spring constants you like. If you track down a bug or something, please report it on redmine.gromacs.org. A workaround of course would be to simply add another window (or windows) with the same original force constant that gives adequate sampling. -Justin
[gmx-users] GROMOS54A8 parameters in GROMACS format
Hello all, Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h Thank you Stephane-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:united atom
Hello, Is it correct for you that in your topolgy file, some atoms have wrong mass (i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN molecule ? Are they at the end ? Stephane -- Message: 3 Date: Thu, 7 Feb 2013 19:13:11 +0330 From: Ali Alizadeh ali.alizadehmoja...@gmail.com Subject: [gmx-users] Re:united atom To: gmx-users gmx-users@gromacs.org Message-ID: capfuhmvnbu3v0verko_faxuvkk0qtg7hgazatjp16-a1rsh...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear Justin Thank you for your reply, I want to use Nose-Hoover thermostat and MTTK barostat and shake algorithm and md-vv integrator, but I got this error: --- Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- A part of my topology file: -- [ moleculetype ] ; Namenrexcl DECANE 9 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 0 LI rtp LI q 0.0 1 opls_071 0 LI C1 1 0 14.027 ; qtot 0 2 opls_071 0 LI C2 2 0 14.027 ; qtot 0 3 opls_071 0 LI C3 3 0 14.027 ; qtot 0 4 opls_071 0 LI C4 4 0 14.027 ; qtot 0 5 opls_071 0 LI C5 5 0 14.027 ; qtot 0 6 opls_071 0 LI C6 6 0 14.027 ; qtot 0 7 opls_068 0 LI C7 7 0 15.035 ; qtot 0 8 opls_071 0 LI C8 8 0 14.027 ; qtot 0 9 opls_068 0 LI C9 9 0 15.035 ; qtot 0 10 opls_071 0 LIC10 10 0 14.027 ; qtot 0 --- On 2/7/13 9:46 AM, Ali Alizadeh wrote: Dear All user There are 350 decane molecules in my simulation box, I like doing a simulation(npt ensemble) by a united atom force field, Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in gromacs? Beside, How can I neglect coloumb interaction(non-bonded) and dihedrals(bonded)? The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA (united-atom) types, so you could in theory use OPLS-UA, but that's a fairly ancient force field. In that case, there are no Coulombic interactions anyway, because the united-atom carbons should not have any charge. If you want to neglect dihedrals, I think you're hacking the force field in a way that makes no sense. -Justin -- Sincerely Ali Alizadeh University of Tehran College of engineering(Fanni) Department of chemical engineering IPE (Institute of Petroleum Engineering) M.Sc Candidate, class of 2013 B.Sc Graduate 2011(University of Tehran,Fanni) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Compute the end to end distance distribution for surfactant
Dear All, I would like to compute the end to end distribution for different parts (i.e. hydrophobic and the polar) of several detergent molecules. I know that g_polystat can do the job and indeed i can obtain the end-to-end distance of the whole molecule (at least for the distance vs. time). But it is not clear to me how to obtain the end to end distance values for the different parts of my molecule with g_polystat. Can you help me ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: pressure_coupling
Hello, This is a very nice and interesting work, Michael. Thank you for the efforts you made in writing this paper. I hope you will publish it. Best Stephane Hi, all- There are some issues with MTTK + constraints that are being worked out for 4.6. The good thing is, I have developed some sensitive tests of the correct volume distribution (see http://arxiv.org/abs/1208.0910) and the errors in PR are very, very small. I would recommend using md + PR for projects with code before 4.6. On Thu, Nov 22, 2012 at 4:27 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: -Urspr?ngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von tarak karmakar Gesendet: Donnerstag, 22. November 2012 10:15 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] pressure_coupling U r right FLorian I have also tried playing around the tau_p but in vain. Even in absence of any constraints, it is giving almost same result. Em thinking to move again to Leap-Frog, NH , PR. I see people generally use this combination a lot. Thanks Tarak Yes, that is right. The reason might be, that it is stable, working with Leap-Frog and implemented in Gromacs. However actually PR does not produce an NpT but an isoenthalpic ensemble. It also does not conform to both pressure virial theorems (see appendix of the Nose paper cited in the Gromacs manual). For this reason it would be very very good, if MTTK would work in Gromacs, because it fulfills all requirements for an NpT ensemble. On the other hand side the deviations vanish in the thermodynamic limit, so if your system is large enough, there should be no significant difference. /Flo On Wed, Nov 21, 2012 at 8:08 PM, Florian Dommert domm...@icp.uni- stuttgart.de wrote: --- Florian Dommert Dipl. Phys. Institut f?r Computerphysik Universit?t Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 -Urspr?ngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von tarak karmakar Gesendet: Mittwoch, 21. November 2012 15:03 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] pressure_coupling Thanks for the information Flo. Before doing NPT I have already equilibrated my system by heating it from 0K to 300K in 300 ps, then the pressure has reached to 1 bar. Now while doing NPT I'm getting the excess pressure. Is there any problem with the coupling constant ? I am checking it by taking different tau_p values. Let's see. I don't think that playing around with the coupling constant will help you. You can set it to extreme values, but you won't see any difference. The coupling constant determines, how fast the system pressure should relax to the reference pressure. I would see a better possibility to play around by simulating for a longer time. Then observing the variation of the pressure in time, the size of the fluctuation and the excess pressure. Perhaps something will change, but I don't think so. I play around with the coupling constants but observed no change. Maybe, but this is really speculation, there is a problem with the combination of constraints and MTTK. Please check the archives of the user and developer list to obtain more information. /Flo On Wed, Nov 21, 2012 at 1:16 AM, Florian Dommert domm...@icp.uni- stuttgart.de wrote: -Urspr?ngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Justin Lemkul Gesendet: Dienstag, 20. November 2012 18:33 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] pressure_coupling On 11/20/12 12:29 PM, tarak karmakar wrote: Thanks Justin for the quick reply. Is there any problem with the algorithms ?? I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE has been used to constrains the H-covalent bonds. tau_t = 1 ps tau_P = 1 ps I got the mean pressure at ~130 bar. Previously with the same initial coordinates I have used Leap-Frog, NH, Parinello-Rehman with LINCS to constrain H-covalent bonds. tau_t was 0.1 ps and tau P was 2 ps. The I have seen the pressure fluctuating around 1 bar( as expected) So can you please inform me from where this problem is coming - algorithms and/ tau_t and tau_P parameters ? I have no personal experience with the md-vv/MTTK combination. The way to test if there is a bug or something is to take an equilibrated system (as suggested before) and continue it with the desired parameters. If they deviate or incorrectly report pressure, then there's probably a bug. I'm not ready to conclude that until it is tested though. -Justin I once tried to use the same
[gmx-users] which version it is
Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] which version it is
Hi Thomas and Justin, I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of the CHARMM36 force field files contain the newly developed parameters for protein (also called CHARMM36) and described in Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles. Journal of Chemical Theory and Computation, 120718184839007. doi:10.1021/ct300400x I said no Sorry if it was not clear in my previous message Stephane -- Message: 1 Date: Mon, 19 Nov 2012 16:14:48 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] which version it is To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af02d1c...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Message: 3 Date: Mon, 19 Nov 2012 16:28:28 + From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa5e2c.4000...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. Cheers Tom ABEL Stephane 175950 wrote: Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Dr Thomas Piggot University of Southampton, UK. -- Message: 4 Date: Mon, 19 Nov 2012 11:34:28 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa5f94.6090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/19/12 11:28 AM, Thomas Piggot wrote: Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. There is indeed a CHARMM36 protein force field that is distinct from the one included in CHARMM27 (which is, as you say, CHARMM22 + CMAP). http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflatNumber=30472 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 5 Date: Mon, 19 Nov 2012 16:48:27 + From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa62db.8010...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed I must have missed that one, thanks for the link! So, to confirm, the protein force field in the CHARMM36 force field contribution is the CHARMM22 protein force field with the CMAP correction. The contribution is just for the updated CHARMM36 lipids. Cheers
[gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield
Hi, CHARMM22star FF is a fork of CHARMM27 ff for proteins with several changes in some diedral parameters. It should be compatible with the others CHARMM parameters for biomolecules. Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)
Hello, Can you explain why you want to use/convert the RB form for your alkane dihedral angles instead of the usual CHARMM dihedral potential form available in charmm force field library available in the GROMACS distribution ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] charge calculation........
Hi Since you want to use the AMBER force for your calculations, you will need to compute the RESP charges for your new residue (unprotoned TYR) and add the charges in your *rtp file. To compute the charges, you can use the RED.Server (http://q4md-forcefieldtools.org/REDS/). It is not easy, so read the tutorials. HTH Stephane -- Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the .rtp file. Now I am bit confused with the charge of the unprotonated one. How can I calculate the partial charges for each and every atoms in unprotonated tyrosine? Would Gaussian/SCF be a good one to deal with this matter? Should I take the tyrosine amino acid alone to calculate the charge in Gaussian ? Please suggest me the proper method(s) to calculate the charge. Thanks, Tarak -- Message: 6 Date: Mon, 17 Sep 2012 08:08:22 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] visualize trajectory To: Shima Arasteh shima_arasteh2...@yahoo.com,Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 505712b6.3030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/17/12 6:57 AM, Shima Arasteh wrote: Hi , Which software is used to visualize a large mdrun output? For example 60 GB trajectory file. I think you should probably have a look at http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume before proceeding. There are several programs that will work, provided you don't exhaust the memory available on your workstation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 7 Date: Mon, 17 Sep 2012 08:10:27 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Regarding RMSD graph nalysis To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50571333.1060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/17/12 7:02 AM, naga sundar wrote: Dear gromacs users I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7 nm and immediate fall was observed. I rerun the 20 ns simulation for the same molecule with same procedure. While analyzing the RMSD sudden increase in the deviation was observed (0.2 nm to 1.7 nm) at the simulation period of ~12 ns. So i want to know the reason For sudden rise and fall in RMSD values. Next, in first MD run this deviation was observed at ~9 ns (0.2 nm to 1.7 nm) but while rerun the molecule with same procedure this deviation was observed at ~12 ns. It sounds to me like your trajectories haven't correctly accounted for periodicity. g_rms does not elegantly handle sudden jumps across the box. You will need to work with trjconv. Usually a simple trjconv -pbc mol -ur compact -center does the trick for a simple protein, but for complexes it is often more difficult. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 8 Date: Mon, 17 Sep 2012 21:48:23 +0900 From: Rajiv Gandhi graji...@gmail.com Subject: Re: [gmx-users] Resuming of calculation from last *.cpt To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: capen9rxbkuf7mzjt8usbzreshwd9amrixh7xbp97ogtdzsb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear all, I have read few papers regarding the photo dissociation event such as Myoglobin heme-ligand bond deletion to induce the photodissociation in MD simulation. Could you please tell me the procedure how can i perform the photodissociation mechanism in Gormacs and which force field have to use, Also I want to study Upon the photo dissociation their structural changes in MD. Thanks in advance, Regards Rajiv -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 101, Issue 48 **-- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Problems with Dihedral transition times for dodecane
Daer all, I am trying to compute the transition times (TT) for all the angles in dodecane in the bulk (216) with gromacs 4.5.5 I have constructed an index file with all angles (C1C2C3C4C9C10C11C12) and for all the nine angles (C*C*C*C*) and use the following command for each angle. ### C1C2C3C4 g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_9_Frac_Dihed.xvg -ot 216_Dodecane_GRO54A7_1_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_1_Avg_Dihed.xvg -b 3000 -e 1 -n 216_Dodecane_.ndx -type dihedral -noperiodic Dih_1.txt up to . ### C9C10C11C12 g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_8_Frac_Dihed.xvg -ot 216_Dodecane_GRO54A7_8_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_8_Avg_Dihed.xvg -b 3000 -e 1 -n216_Dodecane_.ndx -type dihedral -noperiodic Dih_8.txt And for the last one for all angles ### g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_9_Frac_Dihed.xvg -ot 216_Dodecane_GRO54A7_9_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_9_Avg_Dihed.xvg -b 3000 -e 1 -n 216_Dodecane_.ndx -type dihedral -noperiodic Dih_9.txt I obtain the following results for all the dihedral ### C1C2C3C4 Now calculating transitions... Total number of transitions: 28828 Time between transitions:52.464 ps ### C2C3C4C5 Total number of transitions: 29821 Time between transitions:50.717 ps ### C3C4C5C6 Now calculating transitions... Total number of transitions: 33654 Time between transitions:44.941 ps ### C4C5C6C7 Now calculating transitions... Total number of transitions: 32206 Time between transitions:46.961 ps ### C5C6C7C8 Now calculating transitions... Total number of transitions: 31356 Time between transitions:48.234 ps ### C6C7C8C9 Now calculating transitions... Total number of transitions: 34014 Time between transitions:44.465 ps ### C7C8C9C10 Total number of transitions: 31840 Time between transitions:47.501 ps ### C8C9C10C11 Total number of transitions: 31885 Time between transitions:47.434 ps ### C9C10C11C12C13 Total number of transitions: 30362 Time between transitions:49.813 ps And for all the angles in the dodecane Total number of transitions: 90546 Time between transitions:50.110 ps I am confused with these last values, where did they come from ? Why the Total number of transitions (90546): is not the sum of all the previous values. How these values are obtained. Note i have generated the index file for as following: aC* | aC* | aC* | aC* Your advices are welcome. Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] number of gauche - trans transitions with CHARMM36 and AMBER force fields
Dear all, I would like to compute the number of gauche -- trans transitions (per ns) for for several alkanes. I know that I can use g_angle with -ot flag. But in the manual it is stated that this command works only for dihedrals with multiplicity 3. In CHARMM36 force field, for example, the dihedrals parameters have the following form: CTL2CTL2CTL2CTL39 0.000.6778082 ; New CTL2CTL2CTL2CTL39 180.00 0.1966483 ; New CTL2CTL2CTL2CTL39 0.000.43932 4 ; New CTL2CTL2CTL2CTL39 0.000.7405685 ; New CTL2CTL2CTL2CTL29 0.000.4225842 ; New CTL2CTL2CTL2CTL29 180.00 0.5941283 ; New CTL2CTL2CTL2CTL29 0.000.3096164 ; New CTL2CTL2CTL2CTL29 0.000.4058485 ; New So it is possible to use the g_angle functionality with this force field ? Probably I can comment the lines where the angle multiplicity is not equal tp 3 and regenerate a tpr file and use it with g_angle, right ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Hi, Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy between two groups (say NH---CO) by using the Kabsch and Sander function described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637). Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. A good H bond has about -3 kcal/mol binding energy. We choose a generous cutoff to allow for bifurcated H bonds and errors in coordinates and assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., “Hbond(ij)=: [E -0.5kcal/mole].” To obtain HB energy value E, you need only the distance between the donnor and acceptor groups. HTH Stephane -- Message: 2 Date: Thu, 31 May 2012 15:00:05 +0200 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20120531130005.302...@gmx.net Content-Type: text/plain; charset=utf-8 Dear All, I have no clue what specifically you are trying, but I feal bad for all the physicist and quantum chemist whom have provided the software and continued to develop it. Scanning in my free time, it seems a large amount of confusion on what people are trying to do stems from differences in what is taught textbook wise for things. For instance a hydrogen bond to a physicist is an integration over space in 3 dimensions including time and probabilities of occupied spaces (atom position variabilities reflected even more in proteins, ie the necessity of multiple MD runs with different starting conformations), Vs. an organic chemist whom has cut offs, ie angles between two points and set distances between two atoms which generally reflect the means of calculated chemical energies within a range (say 80-90% which represent means, but usually from raw small molecules as determinants), Vs. Biologist whom have tables which either use a set distance and angle and little account of variability over time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino acids, etc... I think with gromacs it is very precise, as even the smallest energies between two interacting atoms is taken into account with accuracy reflected by the force fields used, and how they were derived. Good luck, your going to start seeing more and more a flood of biologist. Stephan Watkins Original-Nachricht Datum: Thu, 31 May 2012 19:54:04 +1000 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it explicitly - which is the case for all the force fields in GROMACS. Could you give some further clarification? What are trying to do? Measuring the strength of a hydrogen bond requires you identify a state with and without it and a path between them over which you can integrate. Mark Cheers, Acoot *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 31 May 2012 4:48 PM *Subject:* Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 4:42 PM, Acoot Brett wrote: Dear All, The value of the energy of the hydrogen bond has relation with distance and angle of the hydrogen bond related atoms. As for in the simulation process, the distance and angle of the hydrogen bond related atoms may change continuously. Will you please let me know based on which formula GROMACS calculated the value of the energy of the hydrogen bonds? There is no such formula used in MD force fields implemented in GROMACS. The only non-bonded interactions are the ones you already know about: electrostatics and VDW. Observables like hydrogen bonds and the hydrophobic effect arise from them. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org
[gmx-users] Re: What is the autocorrelation time
Hi Patrick, Your response is indeed more useful that my previous answer and with interesting links thank for the pointers Stephane -- Message: 4 Date: Fri, 18 May 2012 10:51:35 +0200 From: Patrick Fuchs patrick.fu...@univ-paris-diderot.fr Subject: Re: [gmx-users] What is the autocorrelation time To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fb60d97.3010...@univ-paris-diderot.fr Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chris, I understand your question, this autocorrelation time puzzled me for a long time as well. Not far from the interpretation you give, Scott Feller defines it (http://dx.doi.org/10.1007/978-1-59745-519-0_7) as the time a given observable takes to lose the memory of its previous state, or in other words the time it takes to relax (that's why it's sometimes called relaxation time). He also discusses it as a tool to choose the block size for calculating an error estimate of an observable (one single simulation can be used as independant samples if each block size is autocorrelation time). We also had a nice discussion some years ago on the mailing list on free energy calculation and error estimate: http://lists.gromacs.org/pipermail/gmx-users/2007-May/027281.html. John Chodera pointed me to a useful article from Wolfhard Janke (the link in the discussion is broken, here's the new one: http://www2.fz-juelich.de/nic-series/volume10/janke2.pdf). There you'll find a rigorous mathematical definition of autocorrelation time. Quoting this paper This shows more clearly that only every 2 tau_int iterations the measurements are approximately uncorrelated and gives a better idea of the relevant effective size of the statistical sample (tau_int is the integrated autocorrelation time; as you said the autocorrelation function is usually a single exponential, but sometimes it's more complex and one needs to evaluate it by integration of the autocorrelation function). After all these considerations, the autocorrelation time can be seen as a tool to assess the time that is needed to have a good estimate of an observable: the simulation must be many many times longer than the autocorrelation time. And sometimes it's directly related to experimental observables (i.e. NMR relaxation experiments). Hope it's useful, Patrick Le 16/05/2012 23:39, Christopher Neale a ?crit : Thank you Stephane. Unfortunately, neither of those links contains the information that I am seeking. Those links contain some example plots of autocorrelation functions including a discussion of time-spans over which the example time-series is autocorrelated and when it is not, but neither link defines the (exponential or integral) autocorrelation time except to show a plot and indicate when it is non-zero and when it fluctuates about zero. For example, I already know that the autocorrelation time describes the exponential decay of the correlation and that two values drawn from the same simulation are statistically independent if they are separated by a sufficient number of (accurate) autocorrelation times, but this information is not exactly a definition of the autocorrelation time. I am hoping to find a definition of the autocorrelation time in terms of the probability of drawing uncorrelated samples, although any complete definition will do. If anybody else has the time, I would appreciate it. Thank you, Chris. -- original message -- Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromol?cules Biologiques INTS, INSERM UMR-S665, Universit? Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] What is the autocorrelation time
Hi Chris, Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] amber-lipid
Hi, In my opinion use Amber ff to simulate phospholipids is a bad idea. An alternative is to use GAFF with the good RESP charges. See these papers where several phospholipids are simulated with the GAFF ff. (1) Siu, S. W. I.; Vácha, R.; Jungwirth, P.; Böckmann, R. A.; Shirley, S. W. I.; Robert, V.; Pavel, J.; Rainer, A. B. The Journal of chemical physics 2008, 128, 125103. (2) Rosso, L.; Gould, I. R. J. Comput. Chem. 2008, 29, 24-37. HTH Stephane - Message: 7 Date: Mon, 6 Feb 2012 14:04:21 +0200 From: ??? rayevsk...@gmail.com Subject: [gmx-users] amber-lipid To: gmx-users@gromacs.org Message-ID: cab6cz-kcannphwurmpho_zqdcafknhxej1aa0tjadk+0cek...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Is it possible to use amber forcefield with lipid parameters like it was done with gmx in KALP-15 in DPPC tutorial? I have to use amber forcefield as it is neccessary for parametrization of my ligand and its stecking interactions. Thank you very much -- Nemo me impune lacessit -- Message: 8 Date: Mon, 6 Feb 2012 17:39:54 +0530 From: Anushree Tripathi anushritripa...@gmail.com Subject: Re: [gmx-users] problem with nvt equilibration To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAAx43BzE=yB3FK=2lcktmul9+tmpj_hb6wqrx6ibmd60p8q...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Will you please send me the basic tutorial in which I can find how to use -n option in grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr command. On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anushree Tripathi wrote: where should I use -n option in the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr).Please tell me. I would suggest you refer to grompp -h and/or go through some basic tutorial material so that you can get a feel for command line options and how to apply them. -Justin On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote: On 6/02/2012 8:28 PM, Anushree Tripathi wrote: Inspite of having DPPC in index file,when I run the command ( i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the error: Group DPPC not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Now, what to do? Please guide me. You seem not to have used the -n option. You could try using it. :) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120206/e6fab5df/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Half double pair list method in GROMACS [update]
Hi Sai I am also agree with Christ, your approach seems also correct to me. But don't to forget to test your change to be sure, by doing a single point energy test as it is said in the Christ's message. Good luck Stephane -- Message: 1 Date: Fri, 02 Dec 2011 16:07:19 -0500 From: Chris Neale chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS [update] To: gmx-users@gromacs.org Message-ID: 4ed93e07.5070...@utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; format=flowed What you have done seems alright. I didn't look closely enough to be sure though. One of the good things about this method is that you can easily test it yourself. To do this, create two different .gro files, one containing the atoms from one ff and the other containing the other atoms. For each, do separate zero-step mdrun evaluations of their energies under (a) their original ff, and (b) the combined HEDP ff that you have constructed. The energy evaluations should be the same once you account for rounding errors. Then all that is left is for you to be certain that you didn't cause any problems for nonbonded interactions. Note that you'll need to return to the original atomtypes for the first half of this test. Note that the only thing that the HEDP method is intended to perturb is the 1-4 interactions (and by perturb I mean that they will now be correct). Chris. -- original message -- Hi Stephane Chris, I followed all the threads posted by you two. I have a protein using ff99SB and GLYCAM for sugars. I have a disaccharide bound to protein. In xleap of AMBERTOOLS, I use the GLYCAM and ff99SB to generate the topology and coordinate files. I did the tests as Chris' original posts and by Stephane. The 1-4 interaction terms match for sugar alone and protein alone with HEDP method. When I generate topology and coordinate files with xleap of AMBER, there are three atom types that are common to protein and sugar. The atom types for my case are H1, OH and HO. Since for protein pairtypes using ff99SB, the epsilon has to be divided by 10 and pairs section be replicated five times and for sugar the epsilon in the pairtypes be divided by six and replicated six times, I am a little concerned about the three atomtypes that are common. So what I did was to change the atomtypes of sugar as H1S, OHS HOS for sugar and H1, OH and HO for protein and I made the changes accordingly in the pairtypes section for protein and sugar. Is this a valid approach? Any suggestion will be helpful. To make things little more clear: H1H10. 0. A 2.47135e-01 6.56888e-02 ;originally obtained using amb2gmx.pl H1S H1S 0. 0. A 2.47135e-01 6.56888e-02 ;Glycam Hydrogen of Sugar ( I changed this so that the common atom types be separated) In the ffnonbonded_complex_mod.itp: ;;using combination rule of 2 [ pairtypes ] ;;for protein H1 H1 1 0.247135000 0.006568880 ;the epsilon is divided by 10 ;;for sugar H1S H1S 1 0.24713500 0.010948133 ;the epsilon is divided by 6 Thanks for your time, Regards Sai On Mon, Sep 5, 2011 at 11:33 AM, ABEL Stephane 175950 Stephane.ABEL at cea.frwrote: Dear All, Below a little update and results about the application of half double pair list method to scale properly the Coulombic 1-4 interactions in case of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined. I have followed the 4 steps described in [1] and used the following values in my forcefield.itp file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 0.16 #include ffnonbonded_mod.itp ;#include ffnonbonded.itp #include ffbonded.itp I used two different topology files for the glycolipid (bDM) and the peptide. One with (*_mod.itp) with pair list parameters duplicated 6 times (bDM) and 5 times (peptide) and with single pair list (*_no_mod.itp) as decribed in [1]. TESTING: Three 3 different systems were examined: A. A first system containing 1 glycolipid (bDM) in water cubic box B. A second system with 1 peptide in TIP3P water C. And a third system with 1 peptide and 1 glycolipid in water cubic box To obtain the glycolipid and peptide energy pairs, I did one step of MD in NVT ensemble with the *.mdp file given in [2] with different energygrps and tc_grps. For 1. energygrps and tc_grps = bDM SOL For 2. energygrps and tc_grps = Protein SOL For 3. energygrps and = Protein bDM SOL bDM/water system Test_A1 ## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and the *_no_mod.itp file : ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0
[gmx-users] diffusion of the water at the micelle surface
Hi Chris, Druz Thank you very much for your reply. Indeed I have read several papers where the diffusion of water at the membrane surface have been computed. Since the diffusion of the interfacial water is an useful properties to examine the micelle/surface irregularities, I would hope that this option exist in gromacs. Unfortunately, it is not the case, so i will try your suggestions . Stephane -- Message: 6 Date: Sat, 26 Nov 2011 10:17:10 -0500 From: chris.ne...@utoronto.ca Subject: [gmx-users] diffusion of the water at the micelle surface To: gmx-users@gromacs.org Message-ID: 2026101710.bbl5wl376s04c...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for you. If you don't hear from anybody about how to do this, then I'd suggest that you simply use g_dist to get the time-dependent distance for each water molecule and then use g_traj to output the coordinates of each water molecule and then script it yourself after reading one of the papers where people compute depth-dependent diffusion profiles for a lipid bilayer. Chris. -- original message -- I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or the number of water will change with the simulation time . Thank you for your response Stephane -- Message: 7 Date: Sat, 26 Nov 2011 23:22:59 +0800 From: lina lina.lastn...@gmail.com Subject: Re: [gmx-users] diffusion of the water at the micelle surface To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cag9cjmnxasa7nj+8cgkhavodvobluvzqqruqrcsxzs37m6z...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote: When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for you. If you don't hear from anybody about how to do this, then I'd suggest that you simply use g_dist to get the time-dependent distance for each water molecule and then use g_traj to output the coordinates of each water molecule and then script it yourself after reading one of the papers where people compute depth-dependent diffusion profiles for a lipid bilayer. Chris. -- original message -- I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or the number of water will change with the simulation time . You may try g_density, choose different time interval. Thank you for your response Stephane -- gmx-users mailing list ? ?gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculation of the isothermal compressibility with g_energy for a box with different components.
Hi GMXusers, I know that the g_energy can be used to compute/estimate the adiabatic and isothermal compressibility values of the simulation box when the TEMP, volume and nmol values are given. nmol can be easily given for a pure solvent but when I have a two (or more) different species in the my system how to choose the nmol value to obtain the compressibility of the system. I know that I can also manually obtained the isothermal compressibility value at T manually from the simulation box volume but i would like to use g_energy to verify my results Thanks in advance for your help. Stephane-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Half double pair list method in GROMACS [update]
Dear All, Below a little update and results about the application of half double pair list method to scale properly the Coulombic 1-4 interactions in case of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined. I have followed the 4 steps described in [1] and used the following values in my forcefield.itp file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 0.16 #include ffnonbonded_mod.itp ;#include ffnonbonded.itp #include ffbonded.itp I used two different topology files for the glycolipid (bDM) and the peptide. One with (*_mod.itp) with pair list parameters duplicated 6 times (bDM) and 5 times (peptide) and with single pair list (*_no_mod.itp) as decribed in [1]. TESTING: Three 3 different systems were examined: A. A first system containing 1 glycolipid (bDM) in water cubic box B. A second system with 1 peptide in TIP3P water C. And a third system with 1 peptide and 1 glycolipid in water cubic box To obtain the glycolipid and peptide energy pairs, I did one step of MD in NVT ensemble with the *.mdp file given in [2] with different energygrps and tc_grps. For 1. energygrps and tc_grps = bDM SOL For 2. energygrps and tc_grps = Protein SOL For 3. energygrps and = Protein bDM SOL bDM/water system Test_A1 ## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and the *_no_mod.itp file : ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 1.0 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 bDM-bDM -4.00855e+02 -3.71401e+012.03406e+032.79234e+02 Test_A2 with the topology *_mod.itp file and the directive ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 0.16 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 bDM-bDM -4.00855e+02 -3.71401e+012.03406e+032.79234e+02 Test_A3 with the topology *_no_mod.itp file and the directive ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 0.16 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 bDM-bDM -4.00855e+02 -3.71401e+013.39010e+022.79234e+02 Coul-14 energy for bDM-bDM in Test_A1 = Coul-14 energy in Test_A2 -- OK ! Coul-14 energy for bDM-bDM Test_A3 is 6 smaller than Coul-14 energy in Test_A1 and Test 2 --- OK ! peptide/water system Test_B1 Control with AMBER force field fudgeLJ fudgeQQ parameters, the *_no_mod.itp file ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 0.5 0.8333 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 Protein-Protein -1.49026e+03 -4.12114e+023.80551e+036.55321e+02 Test_B2 Control with the peptide *_no_mod.itp file and the directive ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 0.166 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 Protein-Protein -1.49026e+03 -4.12114e+027.61132e+021.31064e+03 Test_B3 With the peptide *_mod.itp file and the directive ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 0.16 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 Protein-Protein -1.49026e+03 -4.12114e+023.80566e+036.55320e+02 Coul-14 and LJ-14 energies for Protein-Protein in Test_B3 are 5 times Coul-14 and 2 times LJ-14 energies, respectively, than in Test_B1 --- OK ! Coul-14 and LJ-14 energies for Protein-Protein in Test_B3 = Coul-14 and LJ-14 energies in Test_B1 --- OK ! peptide/bDM/water system Test_C1 ## Control with the peptide and the bDM *_mod.itp topology files and the directive ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ## 1 2 yes 1.0 0.16 Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 Protein-Protein -1.48386e+03 -3.99146e+023.79532e+036.53553e+02 bDM-bDM -3.69788e+02 -3.51804e+012.00228e+032.25026e+02 Test_C2 ## Control with the peptide and the bDM *no_mod.itp topology files and the directive Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 Protein-Protein -1.48386e+03 -3.99146e+027.59063e+021.30711e+03 bDM-bDM -3.69788e+02 -3.51804e+013.33713e+022.25026e+02 bDM-bDM Coul-14 energy in Test_C2 is 6 times smaller, respectively, than in the Test_C1 --- OK ! Protein-Protein Coul-14 and LJ1-4 energies
[gmx-users] Half double pair list method in GROMACS
Chris, Thank you for your confirmation. I did the changes. I am currently doing some tests, I will send you a feedback about the results off-list (if you want) shortly. A bientôt Stéphane Message: 1 Date: Thu, 01 Sep 2011 14:38:53 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS To: gmx-users@gromacs.org Message-ID: 20110901143853.537ln0dj94w4w...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed It's a typo, but it's in the discussion and not in the do this part of the method so I decided not to mention it. I don't see another question in this post, so I hope that you have figured things out. Note that I have never tested the exact implementation that I suggested in that April email. It seems like it should work just fine, but it is numerically different than the OPLS/Berger combination so there is no way to be sure until you check the energies as I suggested. I'd be interested to have you report back on the energy matching once you have done the tests. Good luck, Chris. -- original message -- Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how to use the Berger and OPLS force fields together in the same system. By reading carefully the meaning of the gen-pairs directive, I found several errors in my force field. BYW in your previous message http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the step 3, I think there is a typo, it is values/10 instead of values/12. Am I right? Thank you again Stephane Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GROMOS45ACARBO force fields in the GROMACS format.
Dear All, I would like to perform some MD of disaccharides in water using GROMACS and the new ff for sugars GROMOS45ACARBO from Hansen and unenberger(JCC, 32, 6, 2011). Does somebody have these parameters in the GROMACS format (e.g. the *.itp files) and want to share them with me. Thank you in advance. Stéphane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM CNRS URA2096 91191 Saclay, FRANCE URL: http://www.st-abel.com -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] solvation box for say 50mM chaps solution
HI shahid, you can also use the following formula ((N_chaps/(Nw*Vw))/6.02214179)*1=density you want in (Mol) Where - N_chaps is the number of chaps mol. 614.88 g (from wikipedia) - Nw : number of water mol. - Vw : volume of water (30 A3 in ambiant condition) ~ - 6.02214179 Avogadro number - 1 : correction factor I hope this will help S On 18/01/2011 10:33 PM, shahid nayeem wrote: Dear Gmx User I want to prepare a solvation box for say 50mM chaps solution. The density is not known. An aqueous solution has density close to 1g/mL. That's enough to make an estimate of the number of molecules, which you can refine if you don't like the resulting equilibrated size/density/concentration/whatever. Mark How should I start calculating the number of chaps molecule and number of water molecule required for say 6X6X6 size box, which after equilibriation should give the exact strength of the solution. For Urea and guanidinium I know the references and mail archive has many suggestion but how I should proceed with this new solvation box. msnayeem -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 81, Issue 118 ** winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] perfluorohexane pdb
Re hi Marcelo, Below the perfluorohexane molecule in the pdb format construct with the Discovery Studio Visualizer v2.5 REMARK Accelrys Discovery Studio PDB file REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011 HETATM1 C1 0 -11.336 -0.581 0.212 1.00 0.00 C HETATM2 C2 0 -10.035 -0.174 -0.542 1.00 0.00 C HETATM3 C3 0 -8.771 -0.197 0.410 1.00 0.00 C HETATM4 C4 0 -7.458 0.219 -0.369 1.00 0.00 C HETATM5 C5 0 -6.194 0.196 0.583 1.00 0.00 C HETATM6 C6 0 -4.893 0.603 -0.171 1.00 0.00 C HETATM7 F7 0 -11.590 0.293 1.248 1.00 0.00 F HETATM8 F8 0 -11.226 -1.862 0.712 1.00 0.00 F HETATM9 F9 0 -12.391 -0.539 -0.675 1.00 0.00 F HETATM 10 F10 0 -10.216 1.097 -1.046 1.00 0.00 F HETATM 11 F11 0 -9.852 -1.059 -1.582 1.00 0.00 F HETATM 12 F12 0 -8.977 0.685 1.449 1.00 0.00 F HETATM 13 F13 0 -8.613 -1.470 0.913 1.00 0.00 F HETATM 14 F14 0 -7.617 1.493 -0.871 1.00 0.00 F HETATM 15 F15 0 -7.252 -0.663 -1.408 1.00 0.00 F HETATM 16 F16 0 -6.377 1.082 1.623 1.00 0.00 F HETATM 17 F17 0 -6.013 -1.074 1.087 1.00 0.00 F HETATM 18 F18 0 -5.004 1.884 -0.671 1.00 0.00 F HETATM 19 F19 0 -4.639 -0.271 -1.207 1.00 0.00 F HETATM 20 F20 0 -3.839 0.561 0.716 1.00 0.00 F END The structure needs some changes (atom names ?) and minimization steps to relax the structure. hope this helps Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE : gmx-users Digest, Vol 81 , Issue 58
Hi Marcelo, I can send you a pdb file of this molecule construct with Discovery visualizer 2.5 if you are interested. You will need only to change the atom names and a do several minimzation steps. Stephane On Mon, 2011-01-10 at 17:59 +, Marcelo Silva wrote: Hi everybody, I was looking for the structure of perfluorohexane to create the pdb file to use with gromacs but I can't find anywhere. I have also looked in pdb databases. Do you know any paper where the structure is reported? Is it possible to use gromacs to do the geometry optimization? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] perfluorohexane pdb... again
Hi Justin As i have said in the message the pdb file needs probably some (small) changes. emacs (or vi) and vmd or rasmol are our friends ;) Below the pdb file in the correct format (tested with rasmol and vmd) REMARK Accelrys Discovery Studio PDB file REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011 ATOM 1 C1 HEF 0 -11.336 -0.581 0.212 1.00 0.00 C ATOM 2 C2 HEF 0 -10.035 -0.174 -0.542 1.00 0.00 C ATOM 3 C3 HEF 0 -8.771 -0.197 0.410 1.00 0.00 C ATOM 4 C4 HEF 0 -7.458 0.219 -0.369 1.00 0.00 C ATOM 5 C5 HEF 0 -6.194 0.196 0.583 1.00 0.00 C ATOM 6 C6 HEF 0 -4.893 0.603 -0.171 1.00 0.00 C ATOM 7 F7 HEF 0 -11.590 0.293 1.248 1.00 0.00 F ATOM 8 F8 HEF 0 -11.226 -1.862 0.712 1.00 0.00 F ATOM 9 F9 HEF 0 -12.391 -0.539 -0.675 1.00 0.00 F ATOM 10 F10 HEF 0 -10.216 1.097 -1.046 1.00 0.00 F ATOM 11 F11 HEF 0 -9.852 -1.059 -1.582 1.00 0.00 F ATOM 12 F12 HEF 0 -8.977 0.685 1.449 1.00 0.00 F ATOM 13 F13 HEF 0 -8.613 -1.470 0.913 1.00 0.00 F ATOM 14 F14 HEF 0 -7.617 1.493 -0.871 1.00 0.00 F ATOM 15 F15 HEF 0 -7.252 -0.663 -1.408 1.00 0.00 F ATOM 16 F16 HEF 0 -6.377 1.082 1.623 1.00 0.00 F ATOM 17 F17 HEF 0 -6.013 -1.074 1.087 1.00 0.00 F ATOM 18 F18 HEF 0 -5.004 1.884 -0.671 1.00 0.00 F ATOM 19 F19 HEF 0 -4.639 -0.271 -1.207 1.00 0.00 F ATOM 20 F20 HEF 0 -3.839 0.561 0.716 1.00 0.00 F END Stephane Re hi Marcelo, Below the perfluorohexane molecule in the pdb format construct with the Discovery Studio Visualizer v2.5 REMARK Accelrys Discovery Studio PDB file REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011 HETATM1 C1 0 -11.336 -0.581 0.212 1.00 0.00 C HETATM2 C2 0 -10.035 -0.174 -0.542 1.00 0.00 C HETATM3 C3 0 -8.771 -0.197 0.410 1.00 0.00 C HETATM4 C4 0 -7.458 0.219 -0.369 1.00 0.00 C HETATM5 C5 0 -6.194 0.196 0.583 1.00 0.00 C HETATM6 C6 0 -4.893 0.603 -0.171 1.00 0.00 C HETATM7 F7 0 -11.590 0.293 1.248 1.00 0.00 F HETATM8 F8 0 -11.226 -1.862 0.712 1.00 0.00 F HETATM9 F9 0 -12.391 -0.539 -0.675 1.00 0.00 F HETATM 10 F10 0 -10.216 1.097 -1.046 1.00 0.00 F HETATM 11 F11 0 -9.852 -1.059 -1.582 1.00 0.00 F HETATM 12 F12 0 -8.977 0.685 1.449 1.00 0.00 F HETATM 13 F13 0 -8.613 -1.470 0.913 1.00 0.00 F HETATM 14 F14 0 -7.617 1.493 -0.871 1.00 0.00 F HETATM 15 F15 0 -7.252 -0.663 -1.408 1.00 0.00 F HETATM 16 F16 0 -6.377 1.082 1.623 1.00 0.00 F HETATM 17 F17 0 -6.013 -1.074 1.087 1.00 0.00 F HETATM 18 F18 0 -5.004 1.884 -0.671 1.00 0.00 F HETATM 19 F19 0 -4.639 -0.271 -1.207 1.00 0.00 F HETATM 20 F20 0 -3.839 0.561 0.716 1.00 0.00 F END The structure needs some changes (atom names ?) and minimization steps to relax the structure. If you want Gromacs to read this file, it also needs residue names. PDB format is fixed, and this set of coordinates is not correctly formatted, so it will undoubtedly cause problems in Gromacs. -Justin hope this helps Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 81, Issue 60 * winmail.dat-- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] tfe.gro
Hi Hengameh Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously for md. You can easely translated in others ff you use 9 1TFE O11 0.397 1.386 1.484 0.4892 -0.3653 -0.3242 1TFEHO12 0.446 1.346 1.557 0.8382 -0.5070 -0.6322 1TFEH113 0.334 1.332 1.295 1.2033 -0.8553 -0.5343 1TFEH124 0.436 1.209 1.380 2.6521 2.1877 0.2597 1TFE C15 0.355 1.285 1.393 0. -0.4118 -0.0512 1TFEF216 0.186 1.128 1.352 0.1711 -0.0500 0.0270 1TFEF227 0.117 1.302 1.447 -0.1931 0.5088 -0.2066 1TFEF238 0.235 1.159 1.557 0.0214 0.0727 -0.2415 1TFE C29 0.224 1.222 1.439 -0.3522 0.2823 -0.0958 and the TFE.pdb file used to obtain the gro file above ATOM 1 O1 TFE 1 1.9123 -0.2235 0. ATOM 2 HO1 TFE 1 2.7589 0.2000 0. ATOM 3 H11 TFE 1 0.9282 1.3623 -0.8827 ATOM 4 H12 TFE 1 0.9282 1.3623 0.8827 ATOM 5 C1 TFE 1 -0.4189 0.0062 -0. ATOM 6 F21 TFE 1 -1.4055 0.8930 -0. ATOM 7 F22 TFE 1 -0.5650 -0.7556 -1.0660 ATOM 8 F23 TFE 1 -0.5650 -0.7556 1.0660 ATOM 9 C2 TFE 1 0.9031 0.7318 -0. Hope it helps Stefane winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Questions about REMD calculations
Dear all, I come back to you for several questions about the futures replica-exchange calculations that i would like to perform. The system of interest will contain 12 peptides (with 7 residues each) and 4 water molecules, it come from a previous MD performed in NPT ensemble. With these systems, i would like to study the aggregation process between the peptides. After reading several paper about REMD method and playing with the Temperature generator for REMD-simulations web server (http://folding.bmc.uu.se/remd/), i suspect that this system is too big for REMD. Indeed if use the following parameters in the webserver Pdes 0.2 Temperature range 290 - 600 Number of water molecules 41380 Number of protein atoms 1092 Including all H ~ 1656 Number of hydrogens in protein ~ 240 Number of constraints ~ 1092 Number of vsites ~ 0 Number of degrees of freedom ~ 250464 Energy loss due to constraints 520.59 (kJ/mol K) I obtain 271 replicas (ouch !!) . If i assume that for each replica app. 16 CPU, The simulations will be too big and will cost a lot CPU time. So my question is can i reduce safely the number of water in system to reduce the number of replicas ? For example for 1 mol of water the number of replicas will be 135. It is not bad. It is a good option to overcome this limitation. I have also read the number of replicas can be significantly reduced by using variants of REMD for example replica exchange with solute tempering (REST) from Berne and co-workers. Is this method is implemented in GROMACS ? Or Can i use the REMD in implicit solvant for example with the coarse grain OPEP force field as described in Chebaro, et al. (2008).J. Phys. Chem. B 113(1): 267-274. or by Wang and Voth in J. Phys. Chem. B 112(41): 13079-13090. Any advices and comments are welcome Stefane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE : Questions about REMD calcula tions
Dear all, Thank you very much Chris, Xavier and ms (;) for your comments and I will take into account your suggestions in my proposal (for GENCI, Chris ;)) . A bientot Stefane -- Message: 1 Date: Thu, 14 Oct 2010 17:22:38 +0200 From: Florian Dommert domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] Re: g_velacc problem (Florian Dommert) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cb7203e.1020...@icp.uni-stuttgart.de Content-Type: text/plain; charset=ISO-8859-1 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/14/2010 04:41 PM, Eudes Fileti wrote: Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific plane (say xy) using g_velacc? Or it is only possible with g_msd? I am not sure, but the MSD is nothing else than the integrated VACF, so if you modify the code correspondingly it should work. The modification shouldn't be that hard, because you just have to prevent summing up a certain direction of the velocity. /Flo Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAky3ID4ACgkQLpNNBb9GiPkK2QCg3gMovcfuJRdOd9+IZ7KrmZ1u 2VgAoIPTQGVxyrmDUXi5PbPPg5tCr7h2 =PBOI -END PGP SIGNATURE- -- Message: 2 Date: Thu, 14 Oct 2010 17:54:02 +0200 From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Questions about REMD calculations To: gmx-users@gromacs.org Message-ID: f654b3ee96986e4b8dc6ef0919c88da301038...@loderi.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 Dear all, I come back to you for several questions about the futures replica-exchange calculations that i would like to perform. The system of interest will contain 12 peptides (with 7 residues each) and 4 water molecules, it come from a previous MD performed in NPT ensemble. With these systems, i would like to study the aggregation process between the peptides. After reading several paper about REMD method and playing with the Temperature generator for REMD-simulations web server (http://folding.bmc.uu.se/remd/), i suspect that this system is too big for REMD. Indeed if use the following parameters in the webserver Pdes 0.2 Temperature range 290 - 600 Number of water molecules 41380 Number of protein atoms 1092 Including all H ~ 1656 Number of hydrogens in protein ~ 240 Number of constraints ~ 1092 Number of vsites ~ 0 Number of degrees of freedom ~ 250464 Energy loss due to constraints 520.59 (kJ/mol K) I obtain 271 replicas (ouch !!) . If i assume that for each replica app. 16 CPU, The simulations will be too big and will cost a lot CPU time. So my question is can i reduce safely the number of water in system to reduce the number of replicas ? For example for 1 mol of water the number of replicas will be 135. It is not bad. It is a good option to overcome this limitation. I have also read the number of replicas can be significantly reduced by using variants of REMD for example replica exchange with solute tempering (REST) from Berne and co-workers. Is this method is implemented in GROMACS ? Or Can i use the REMD in implicit solvant for example with the coarse grain OPEP force field as described in Chebaro, et al. (2008).J. Phys. Chem. B 113(1): 267-274. or by Wang and Voth in J. Phys. Chem. B 112(41): 13079-13090. Any advices and comments are welcome Stefane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com http://www.st-abel.com/ -- -- Message: 3 Date: Thu, 14 Oct 2010 12:16:35 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Questions about REMD calculations To: gmx-users@gromacs.org Message-ID: 20101014121635.bg1lkn1bswkks...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Stefane, why are you hesitant to reduce the size of your system. If you can still address the same questions with a smaller system, then I'd say the answer is nearly always to use that smaller system (REMD or not). Besides, my gut feeling is that even if you had enough 271*16 cpus available, you would not get enough exchanges within a reasonable wall clock time to get a converged answer. I say this because you're basically
[gmx-users] REMD speed calculation compared to classical MD
Dear All, For a futur project, I would like to perform the REMD calculations with GROMACS4.5.X. To have an estimation of CPU time required, I have a naive question: What is the speed of REMD compared to a classic NPT MD ? I am aware that the response depends a lot of factor (number of replica, etc.), but since i have no idea and experience with this type of MD, I ask the question ;). The system will have approximatively 25000 atoms. Previously for this system, I got 11 ns/day on 32 CPU for a NPT MD with GROMOS53A6 and GMX4.0.5. Thanks you in advance for your response. Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD speed calculation compared to classical MD
Thank you all for all your interesting comments. I have now an idea how to write my proposal. A bientôt Stefane Message: 2 Date: Wed, 13 Oct 2010 14:38:54 -0400 From: Chris Neale chris.ne...@utoronto.ca Subject: [gmx-users] REMD speed calculation compared to classical MD To: gmx-users@gromacs.org Message-ID: 4cb5fcbe.2080...@utoronto.ca Content-Type: text/plain; charset=iso-8859-1 Stefane, If you are asking for a comparison of simulation time required, then that is not something that can be answered in the abstract. There are even cases in which REMD will take more total simulation time to converge the 300K ensemble than will N simulations all at 300K. The efficiency of REMD will be highly dependent on the size of the important energy barriers. REMD becomes more efficient than MD as the barriers get higher. To take that to an extreme, if you wanted to know the distribution of x-coordinate values of one specific water molecule in a box of pure water, REMD with 100 replicas would be 100 times less efficient than simple MD -- there are no energy barriers and so the 99 replicas at temperatures above 300K are a total waste of time. At the other extreme, if your energy barrier is 30 Kcal/mol at 300K, then you will essentially never cross it at 300K and REMD, if it works, will be infinitely more efficient because the replica at 300K will essentially never sample the other side of that barrier. There have been a few comparisons, but I don;t know of any general rule that you can apply here. On 10/13/10 7:42 PM, XAvier Periole wrote: / // Well the exchanges do not cost time ... so basically each replica runs // at the speed it would run it was a regular simulation on the number of // cpu you give each replica. // // I do not think there any significant difference in NPT/NVT simulations. // Note NVT is often used for REMD /It us, but that gives high pressure at high T, which is typically not what you want. If you use NPT REMD than the run time between exchanges is in general equal to that of the coldest replica, since that will be at the highest density (unless you go below the density maximum of water :)). / // XAvier. // // On Oct 13, 2010, at 11:36 AM, ABEL Stephane 175950 wrote: // // Dear All, // // For a futur project, I would like to perform the REMD calculations // with GROMACS4.5.X. To have an estimation of CPU time required, I have // a naive question: What is the speed of REMD compared to a classic NPT // MD ? I am aware that the response depends a lot of factor (number of // replica, etc.), but since i have no idea and experience with this type // of MD, I ask the question ;). // // The system will have approximatively 25000 atoms. Previously for this // system, I got 11 ns/day on 32 CPU for a NPT MD with GROMOS53A6 and // GMX4.0.5. // // Thanks you in advance for your response. // // Stefane // // -- // gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users // http://lists.gromacs.org/mailman/listinfo/gmx-users // Please search the archive at // http://www.gromacs.org/Support/Mailing_Lists/Search before posting! // Please don't post (un)subscribe requests to the list. Use the // www interface or send it togmx-users-request at gromacs.org. http://lists.gromacs.org/mailman/listinfo/gmx-users // Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists // / -- David. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101013/f8132c5f/attachment-0001.html winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error : There is no domain decomposition for 4 nodes that compatible with the given box
Dear All, I am trying to do a MD of a system containing TIP3P water, a peptide, some glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and are taken from previous MD. The bonded and nonbonded parameters was converted in GROMACS manually because some parameters are not in present in current GMX (v 4.5.1) distribution. I have minimized successfully the system. see below em.mdp --- title = bDM+KTM17 in water ; Preprocessor - specify a full path if necessary. cpp = cpp include = -I../top define = -DFLEXIBLE integrator = steep nstcgsteep = 5000 emstep = 0.01 emtol = 500.0 ;dt = 0.002 pbc = xyz nsteps = 5000 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 optimize_fft = yes --- Final results of energy minimization process Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06 Coul. recip. Potential Pressure (bar) -1.17090e+05 -9.67347e+05 0.0e+00 Steepest Descents converged to Fmax 500 in 107 steps Potential Energy = -9.67347283476003e+05 Maximum force = 4.75153618041724e+02 on atom 313 Norm of force = 9.37591893853129e+00 But when i try to equilibrate this system in NVT ensemble for 100 ps with the md.mdp below nvt.mdp --- title = KTM17-bDM MD ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdw-type = cut-off ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; one coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed - I obtain the following error with mdrun_mpi command /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g hMRP1_K-TM17_bDM_h2o_Cl_md.log -- error Initializing Domain Decomposition on 4 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107 multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106 Minimum cell size due to bonded interactions: 7.402 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm Estimated maximum distance required for P-LINCS: 0.819 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun_mpi, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.25216 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Player Sleeps With the Fishes (Ein Bekanntes Spiel Von ID Software) I have also checked the mimized structure at different minimization step, and I saw no
[gmx-users] Error : There is no domain decomposition for
Yeah Justin, I have already read the comments related to the link before to post in the mailing list. But I don't know how to correct this ? Increase/decrease the number of node or CPU ? Thank you again for your help Stephane ABEL Stephane 175950 wrote: Dear All, I am trying to do a MD of a system containing TIP3P water, a peptide, some glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and are taken from previous MD. The bonded and nonbonded parameters was converted in GROMACS manually because some parameters are not in present in current GMX (v 4.5.1) distribution. I have minimized successfully the system. see below em.mdp --- title = bDM+KTM17 in water ; Preprocessor - specify a full path if necessary. cpp = cpp include = -I../top define = -DFLEXIBLE integrator = steep nstcgsteep = 5000 emstep = 0.01 emtol = 500.0 ;dt = 0.002 pbc = xyz nsteps = 5000 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 optimize_fft = yes --- Final results of energy minimization process Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06 Coul. recip. Potential Pressure (bar) -1.17090e+05 -9.67347e+05 0.0e+00 Steepest Descents converged to Fmax 500 in 107 steps Potential Energy = -9.67347283476003e+05 Maximum force = 4.75153618041724e+02 on atom 313 Norm of force = 9.37591893853129e+00 But when i try to equilibrate this system in NVT ensemble for 100 ps with the md.mdp below nvt.mdp --- title = KTM17-bDM MD ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdw-type = cut-off ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; one coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed - I obtain the following error with mdrun_mpi command /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g hMRP1_K-TM17_bDM_h2o_Cl_md.log -- error Initializing Domain Decomposition on 4 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107 multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106 Minimum cell size due to bonded interactions: 7.402 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm Estimated maximum distance required for P-LINCS: 0.819 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun_mpi, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.25216 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details
[gmx-users] Re: Error : There is no domain decomposition for ....
Mark, These long range parameters have been used by Bjelkmar et al. in their recent paper [1]for simulations of CHARMM ff in GROMACS. So I use it ! [1] Bjelkmar, P., P. Larsson, et al. (2010). Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. J. Chem. Theory Comput. 6(2): 459-466. Yeah Justin, I have already read the comments related to the link before to post in the mailing list. But I don't know how to correct this ? Increase/decrease the number of node or CPU ? Thank you again for your help Stephane ABEL Stephane 175950 wrote: Dear All, I am trying to do a MD of a system containing TIP3P water, a peptide, some glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and are taken from previous MD. The bonded and nonbonded parameters was converted in GROMACS manually because some parameters are not in present in current GMX (v 4.5.1) distribution. I have minimized successfully the system. see below em.mdp --- title = bDM+KTM17 in water ; Preprocessor - specify a full path if necessary. cpp = cpp include = -I../top define = -DFLEXIBLE integrator = steep nstcgsteep = 5000 emstep = 0.01 emtol = 500.0 ;dt = 0.002 pbc = xyz nsteps = 5000 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 optimize_fft = yes --- Final results of energy minimization process Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06 Coul. recip. Potential Pressure (bar) -1.17090e+05 -9.67347e+05 0.0e+00 Steepest Descents converged to Fmax 500 in 107 steps Potential Energy = -9.67347283476003e+05 Maximum force = 4.75153618041724e+02 on atom 313 Norm of force = 9.37591893853129e+00 But when i try to equilibrate this system in NVT ensemble for 100 ps with the md.mdp below nvt.mdp --- title = KTM17-bDM MD ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching vdw-type = cut-off ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; one coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed - I obtain the following error with mdrun_mpi command /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g hMRP1_K-TM17_bDM_h2o_Cl_md.log -- error Initializing Domain Decomposition on 4 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107 multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106 Minimum cell size due to bonded interactions: 7.402 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm Estimated maximum distance required for P-LINCS: 0.819 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm The maximum allowed
[gmx-users] RE : gmx-users Digest, Vol 77 , Issue 201
OK Mark and Justin, thank you for the pointer I will take a look about it A bientot Stephane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- De: gmx-users-boun...@gromacs.org de la part de gmx-users-requ...@gromacs.org Date: jeu. 30/09/2010 13:56 À: gmx-users@gromacs.org Objet : gmx-users Digest, Vol 77, Issue 201 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: Error : There is no domain decomposition for (Mark Abraham) 2. Re: NAMD simulation in Gromacs (Mark Abraham) -- Message: 1 Date: Thu, 30 Sep 2010 21:48:05 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: Error : There is no domain decomposition for To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: fbd7dfad5f039.4ca50...@anu.edu.au Content-Type: text/plain; charset=us-ascii - Original Message - From: ABEL Stephane 175950 stephane.a...@cea.fr Date: Thursday, September 30, 2010 21:43 Subject: [gmx-users] Re: Error : There is no domain decomposition for To: gmx-users@gromacs.org Mark, These long range parameters have been used by Bjelkmar et al. in their recent paper [1]for simulations of CHARMM ff in GROMACS. So I use it ! [1] Bjelkmar, P., P. Larsson, et al. (2010). Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. J. Chem. Theory Comput. 6(2): 459-466. I'm not questioning any .mdp file settings. However the combination of topology and initial coordinates contains some kind of bonded interaction between atoms that are much further apart than you would normally suppose. You should explore what is going on there. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100930/62c76cfd/attachment-0001.html -- Message: 2 Date: Thu, 30 Sep 2010 21:55:04 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] NAMD simulation in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: fbb29fd25ceae.4ca50...@anu.edu.au Content-Type: text/plain; charset=us-ascii - Original Message - From: oguz gurbulak gurbulako...@yahoo.com Date: Thursday, September 30, 2010 21:38 Subject: [gmx-users] NAMD simulation in Gromacs To: gmx-users@gromacs.org --- |Dear All, I performed a 50 ns md simulation using NAMD and want to continue this simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation in Gromacs ? If so, could you please give me the information about this process ? Not really. You would need to generate a .top in the normal way, and this process cannot use any topology information that NAMD was using. You could start the GROMACS simulation from the endpoint of the NAMD simulation, but it would not be continuous in any sense. Secondly can I convert NAMD output files into gromacs output files and use gromacs analysis tools ? Could you please also give me the information about this issue ? If you have VMD installed then GROMACS is supposed to be able to link to its libraries to enable GROMACS tools to read any file format that VMD can read, which will include all NAMD formats. I'm unaware that anybody has written any documentation about this, however. That's probably the path of least resistance. Mark | --- -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100930/9995bb04/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 77, Issue 201 ** winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un
[gmx-users] Re: A common error Atom O11 in residue bDM 1 was
OK you thank Justin for your explanation. Accordingly, I have changed the C*
and O* atom names in the pdb and now it works.
A bientôt
Stefane
ABEL Stephane 175950 wrote:
You are right Justin,
The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
this problem happens ? Should I change the name of these atoms in the rtp and
pdb files ? Is a trick is available to avoid this bad translation ?
The only option is to not use digits as the first characters in an atom name.
The code in pdb2gmx.c calls a function rename_atoms in xlate.c, which (since a
value of TRUE is passed to the function for bReorderNum), shifts the position of
all digits in the first position:
if (bReorderNum)
{
if (isdigit(atombuf[0]))
{
c = atombuf[0];
for (i=0; ((size_t)istrlen(atombuf)-1); i++)
{
atombuf[i] = atombuf[i+1];
}
atombuf[i] = c;
bReorderedNum = TRUE;
}
}
I think the purpose is really to deal with hydrogens (i.e. 1HG1, etc) but
affects all atoms, as written. A check could probably be implemented to
determine if the atom is H or not, but really might not be worth the effort,
since the vast majority of all structures that will be passed to pdb2gmx will
follow the normal route of: character first, then digits.
-Justin
Stefane
ABEL Stephane 175950 wrote:
Dear all,
I have a very common problem when I try to convert a pdb file to a gro
file with the following command.
I use charmm27ff and gmx4.5.1.
pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
I obtain the following commun error :
Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms
while sorting atoms.
I am surprised to have this message, since after verification in the
1-bDM.pdb, I have not found an atom with this name. I have also checked the
format of the pdb and all the fields are in right place.
Probably atom 1O1 is being translated as O11. I have had similar problems
with translated atom names. If you add -debug 1 to your pdb2gmx command
line, you will get output .pdb files containing the structure as pdb2gmx is
interpreting it. That's how I've identified some spurious translations
before.
-Justin
Below my PDB file ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361
0.30 0.00 ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10
0.00 ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00
ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 ATOM
5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 ATOM 6 1O2
bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 ATOM 7 H2OA bDM
1 -28.731 -10.800 -5.827 0.43 0.00 ATOM 8 1C3 bDM 1
-29.990 -8.385 -6.493 0.14 0.00 ATOM 9 H3A bDM 1 -29.086
-8.411 -7.139 0.09 0.00 ATOM 10 1O3 bDM 1 -31.239 -8.585
-7.237 -0.66 0.00 ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035
0.43 0.00 ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14
0.00 ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00
ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 ATOM
15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 ATOM 16 1C5
bDM 1 -28.865 -6.650 -5.081 0.10 0.00 ATOM 17 H5A bDM
1 -27.963 -7.009 -5.622 0.10 0.00 ATOM 18 1C6 bDM 1
-28.730 -5.254 -4.552 0.05 0.00 ATOM 19 H61A bDM 1 -29.694
-5.009 -4.056 0.09 0.00 ATOM 20 H61B bDM 1 -28.509 -4.622
-5.438 0.09 0.00 ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684
-0.66 0.00 ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43
0.00 ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00
ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 ATOM
25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 ATOM 26 2C2
bDM 1 -24.806 -9.283 -2.026 0.14 0.00 ATOM 27 H2B bDM
1 -24.867 -8.235 -1.662 0.09 0.00 ATOM 28 2O2 bDM 1
-24.477 -10.097 -0.884 -0.66 0.00 ATOM 29 H2OB bDM 1 -23.792
-9.775 -0.294 0.43 0.00 ATOM 30 2C3 bDM 1 -26.163 -9.642
-2.661 0.14 0.00 ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098
0.09 0.00 ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66
0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00
ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 ATOM
35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 ATOM 36 2C5
bDM 1 -25.089 -8.936 -4.892 0.25 0.00 ATOM 37 H5B bDM
1 -24.906 -9.942 -5.326 0.09 0.00 ATOM 38 2C6 bDM 1
-25.225 -7.980 -6.074 0.05 0.00 ATOM 39 H62A bDM 1 -25.159
-6.910 -5.780 0.09 0.00 ATOM 40 H62B bDM 1
[gmx-users] A common error Atom O11 in residue bDM 1 was
You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this bad translation ? Stefane ABEL Stephane 175950 wrote: Dear all, I have a very common problem when I try to convert a pdb file to a gro file with the following command. I use charmm27ff and gmx4.5.1. pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp I obtain the following commun error : Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms while sorting atoms. I am surprised to have this message, since after verification in the 1-bDM.pdb, I have not found an atom with this name. I have also checked the format of the pdb and all the fields are in right place. Probably atom 1O1 is being translated as O11. I have had similar problems with translated atom names. If you add -debug 1 to your pdb2gmx command line, you will get output .pdb files containing the structure as pdb2gmx is interpreting it. That's how I've identified some spurious translations before. -Justin Below my PDB file ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361 0.30 0.00 ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10 0.00 ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00 ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 ATOM 5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 ATOM 6 1O2 bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 ATOM 7 H2OA bDM 1 -28.731 -10.800 -5.827 0.43 0.00 ATOM 8 1C3 bDM 1 -29.990 -8.385 -6.493 0.14 0.00 ATOM 9 H3A bDM 1 -29.086 -8.411 -7.139 0.09 0.00 ATOM 10 1O3 bDM 1 -31.239 -8.585 -7.237 -0.66 0.00 ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035 0.43 0.00 ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14 0.00 ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00 ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 ATOM 15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 ATOM 16 1C5 bDM 1 -28.865 -6.650 -5.081 0.10 0.00 ATOM 17 H5A bDM 1 -27.963 -7.009 -5.622 0.10 0.00 ATOM 18 1C6 bDM 1 -28.730 -5.254 -4.552 0.05 0.00 ATOM 19 H61A bDM 1 -29.694 -5.009 -4.056 0.09 0.00 ATOM 20 H61B bDM 1 -28.509 -4.622 -5.438 0.09 0.00 ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684 -0.66 0.00 ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43 0.00 ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00 ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 ATOM 25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 ATOM 26 2C2 bDM 1 -24.806 -9.283 -2.026 0.14 0.00 ATOM 27 H2B bDM 1 -24.867 -8.235 -1.662 0.09 0.00 ATOM 28 2O2 bDM 1 -24.477 -10.097 -0.884 -0.66 0.00 ATOM 29 H2OB bDM 1 -23.792 -9.775 -0.294 0.43 0.00 ATOM 30 2C3 bDM 1 -26.163 -9.642 -2.661 0.14 0.00 ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098 0.09 0.00 ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66 0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00 ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 ATOM 35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 ATOM 36 2C5 bDM 1 -25.089 -8.936 -4.892 0.25 0.00 ATOM 37 H5B bDM 1 -24.906 -9.942 -5.326 0.09 0.00 ATOM 38 2C6 bDM 1 -25.225 -7.980 -6.074 0.05 0.00 ATOM 39 H62A bDM 1 -25.159 -6.910 -5.780 0.09 0.00 ATOM 40 H62B bDM 1 -26.236 -8.045 -6.532 0.09 0.00 ATOM 41 2O5 bDM 1 -24.218 -8.289 -7.105 -0.66 0.00 ATOM 42 H5OB bDM 1 -24.661 -8.895 -7.704 0.43 0.00 ATOM 43 2O4 bDM 1 -24.011 -8.432 -4.077 -0.40 0.00 ATOM 44 2O1 bDM 1 -22.364 -8.895 -2.386 -0.30 0.00 ATOM 45 C7 bDM 1 -21.159 -9.105 -3.148 -0.11 0.00 ATOM 46 H7A bDM 1 -20.922 -10.188 -3.228 0.09 0.00 ATOM 47 H7B bDM 1 -21.320 -8.848 -4.217 0.09 0.00 ATOM 48 C8 bDM 1 -19.961 -8.389 -2.410 -0.18 0.00 ATOM 49 H8A bDM 1 -19.829 -8.778 -1.378 0.09 0.00 ATOM 50 H8B bDM 1 -20.171 -7.300 -2.464 0.09 0.00 ATOM 51 C9 bDM 1 -18.547 -8.641 -3.005 -0.18 0.00 ATOM 52 H9A bDM 1 -18.718 -8.465 -4.089 0.09 0.00 ATOM 53 H9B bDM 1 -18.415 -9.744 -3.010 0.09 0.00 ATOM 54 C10 bDM 1 -17.452 -7.785 -2.397 -0.18 0.00 ATOM 55 H10A bDM 1 -16.675 -7.915 -3.180 0.09 0.00 ATOM 56 H10B bDM 1 -17.700 -6.702 -2.407 0.09 0.00
[gmx-users] CHARMM - gromacs epsilon and sigma conversiion
Thank you !!! Jianhui Stefane -- Message: 5 Date: Fri, 24 Sep 2010 14:18:25 -0600 From: Jianhui Tian jianhuit...@gmail.com Subject: [gmx-users] CHARMM - gromacs epsilon and sigma conversiion To: gmx-users@gromacs.org Message-ID: aanlktik8xpfhf66l78uxshh7tv6xfhretc8hhbwja...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 eps(charmm)*4.184=epsilon(Gromacs) 0.15*4.184=0.6276 Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs) 2.27*2/(2^(1/6))=0.404468(nm) Cheers, Jianhui Date: Fri, 24 Sep 2010 15:55:44 +0200 From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] CHARMM - gromacs epsilon and sigma conversiion factors To: gmx-users@gromacs.org Message-ID: f654b3ee96986e4b8dc6ef0919c88da301038...@loderi.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 Hi all, I would like to add new atom types in the charmm27.ff for futures simulations of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in GROMACS format. However, I am little puzzled with the vdW paramaters. I would like to know how to convert them (i.e. what are the conversion factors used to convert the CHARMM sigma and epsilon parameters to gromacs sigma and epsilon values ?). For example for the chloride atom CLA CHARMM 27 ; atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 CLA 0.0 -0.150 2.27 ! chloride GROMACS ffcharmmnb.itp ;name at.num mass charge ptype sigma epsilon CLA 17 35.45 -1.00 A 0.404468018036 0.6276 Thanks in advance for your help Stefane -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] A common error Atom O11 in residue bDM 1 was not found in rtp entry
Dear all, I have a very common problem when I try to convert a pdb file to a gro file with the following command. I use charmm27ff and gmx4.5.1. pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp I obtain the following commun error : Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms while sorting atoms. I am surprised to have this message, since after verification in the 1-bDM.pdb, I have not found an atom with this name. I have also checked the format of the pdb and all the fields are in right place. Below my PDB file ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361 0.30 0.00 ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10 0.00 ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00 ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 ATOM 5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 ATOM 6 1O2 bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 ATOM 7 H2OA bDM 1 -28.731 -10.800 -5.827 0.43 0.00 ATOM 8 1C3 bDM 1 -29.990 -8.385 -6.493 0.14 0.00 ATOM 9 H3A bDM 1 -29.086 -8.411 -7.139 0.09 0.00 ATOM 10 1O3 bDM 1 -31.239 -8.585 -7.237 -0.66 0.00 ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035 0.43 0.00 ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14 0.00 ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00 ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 ATOM 15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 ATOM 16 1C5 bDM 1 -28.865 -6.650 -5.081 0.10 0.00 ATOM 17 H5A bDM 1 -27.963 -7.009 -5.622 0.10 0.00 ATOM 18 1C6 bDM 1 -28.730 -5.254 -4.552 0.05 0.00 ATOM 19 H61A bDM 1 -29.694 -5.009 -4.056 0.09 0.00 ATOM 20 H61B bDM 1 -28.509 -4.622 -5.438 0.09 0.00 ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684 -0.66 0.00 ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43 0.00 ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00 ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 ATOM 25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 ATOM 26 2C2 bDM 1 -24.806 -9.283 -2.026 0.14 0.00 ATOM 27 H2B bDM 1 -24.867 -8.235 -1.662 0.09 0.00 ATOM 28 2O2 bDM 1 -24.477 -10.097 -0.884 -0.66 0.00 ATOM 29 H2OB bDM 1 -23.792 -9.775 -0.294 0.43 0.00 ATOM 30 2C3 bDM 1 -26.163 -9.642 -2.661 0.14 0.00 ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098 0.09 0.00 ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66 0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00 ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 ATOM 35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 ATOM 36 2C5 bDM 1 -25.089 -8.936 -4.892 0.25 0.00 ATOM 37 H5B bDM 1 -24.906 -9.942 -5.326 0.09 0.00 ATOM 38 2C6 bDM 1 -25.225 -7.980 -6.074 0.05 0.00 ATOM 39 H62A bDM 1 -25.159 -6.910 -5.780 0.09 0.00 ATOM 40 H62B bDM 1 -26.236 -8.045 -6.532 0.09 0.00 ATOM 41 2O5 bDM 1 -24.218 -8.289 -7.105 -0.66 0.00 ATOM 42 H5OB bDM 1 -24.661 -8.895 -7.704 0.43 0.00 ATOM 43 2O4 bDM 1 -24.011 -8.432 -4.077 -0.40 0.00 ATOM 44 2O1 bDM 1 -22.364 -8.895 -2.386 -0.30 0.00 ATOM 45 C7 bDM 1 -21.159 -9.105 -3.148 -0.11 0.00 ATOM 46 H7A bDM 1 -20.922 -10.188 -3.228 0.09 0.00 ATOM 47 H7B bDM 1 -21.320 -8.848 -4.217 0.09 0.00 ATOM 48 C8 bDM 1 -19.961 -8.389 -2.410 -0.18 0.00 ATOM 49 H8A bDM 1 -19.829 -8.778 -1.378 0.09 0.00 ATOM 50 H8B bDM 1 -20.171 -7.300 -2.464 0.09 0.00 ATOM 51 C9 bDM 1 -18.547 -8.641 -3.005 -0.18 0.00 ATOM 52 H9A bDM 1 -18.718 -8.465 -4.089 0.09 0.00 ATOM 53 H9B bDM 1 -18.415 -9.744 -3.010 0.09 0.00 ATOM 54 C10 bDM 1 -17.452 -7.785 -2.397 -0.18 0.00 ATOM 55 H10A bDM 1 -16.675 -7.915 -3.180 0.09 0.00 ATOM 56 H10B bDM 1 -17.700 -6.702 -2.407 0.09 0.00 ATOM 57 C11 bDM 1 -16.987 -8.238 -1.043 -0.18 0.00 ATOM 58 H11A bDM 1 -16.658 -9.299 -1.039 0.09 0.00 ATOM 59 H11B bDM 1 -17.874 -8.295 -0.376 0.09 0.00 ATOM 60 C12 bDM 1 -15.798 -7.399 -0.595 -0.18 0.00 ATOM 61 H12A bDM 1 -16.131 -6.343 -0.678 0.09 0.00 ATOM 62 H12B bDM 1 -14.966 -7.559 -1.314 0.09 0.00 ATOM 63 C13 bDM 1 -15.271 -7.639 0.808 -0.18 0.00 ATOM 64 H13A bDM 1 -15.139 -8.740 0.874 0.09 0.00 ATOM 65 H13B bDM 1 -15.946 -7.348 1.641 0.09 0.00 ATOM 66 C14 bDM 1 -13.783 -7.068 1.047 -0.18
[gmx-users] CHARMM - gromacs epsilon and sigma conversiion factors
Hi all, I would like to add new atom types in the charmm27.ff for futures simulations of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in GROMACS format. However, I am little puzzled with the vdW paramaters. I would like to know how to convert them (i.e. what are the conversion factors used to convert the CHARMM sigma and epsilon parameters to gromacs sigma and epsilon values ?). For example for the chloride atom CLA CHARMM 27 ; atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 CLA 0.0 -0.150 2.27 ! chloride GROMACS ffcharmmnb.itp ;name at.num mass charge ptype sigma epsilon CLA 17 35.45 -1.00 A 0.404468018036 0.6276 Thanks in advance for your help Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] charmm to gromacs nonbonded parameters after conversion
Hi GMX users, I would like to perform MD with new developped CHARMM parameters in GROMACS. Since these parameters are new, they are not presents in the ffcharm*.itp files given in the of charmm27.ff in the latest GMX distribution. So I have already made the conversions for the bonded parameters. In case of the nonbonded parameters, I have added the LJ values for the new atom types at the end of the NONBONDED section of a par_all_27_lipid.prm file downloaded from the CHARMM website. To convert the LJ values in GROMACS format, I used the perl script of M. Abraham : convert_charmm_to_gromacs.pl (v.1.3) as follow : perl convert_charmm_to_gromacs.pl par_all27_lipid.prm I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected. In the ffcharmmnb.itp the [ atomtypes ] section is present but not the [ pairtypes ] section. Moreover the values in the [ atomtypes ] are different compared to same file given in latest GMX distrib (see below). Why these differences ? - My ffcharmmnb.itp file [ atomtypes ] ;name mass charge ptype c6 c12 CTL1 12.011000 0.0 A -0.001485 -6.588e-06 ; -0.000252 -3.793e-07 CTL2 12.011000 0.0 A -0.001978 -4.173e-06 ; -0.000252 -3.793e-07 CTL3 12.011000 0.0 A -0.003011 -6.944e-06 ; -0.000252 -3.793e-07 CTL5 12.011000 0.0 A -0.003274 -8.007e-06 ; -0.000252 -3.793e-07 CEL1 12.011000 0.0 A -0.003035 -8.095e-06 -- GROMACS 4.5.1 ffcharmmnb.itp [ atomtypes ] ;name at.num mass charge ptype sigma epsilon CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 CTL2 6 12.01100 0.05 A 0.358141284692 0.234304 CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472 CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 . Thank in advance for your halp Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to center molecules in the box with trjconv ?
It works !!! Thank you Justin A bientôt Stefane ABEL Stephane 175950 wrote: Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the peptide located at the micelle interface. Now I would like to plot some MD configs in a PDB format some configs where the micelle and the peptide are placed in the center of the box. To take into account the PBC and to obtain the PDB, for the last frame at 150 ns as I used trjconv with the following commands: 1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump -b 15 -e 15 -o traj_KTM17_DPC_0ns_noJump.pdb With non-SOL (DPC and peptide) as a group for output and where traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation 2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro -center -o traj_KTM17_DPC_0ns_noJump_center.pdb With DPC as a group for centering and System (DPC and peptide) as a group for output. the *.gro file contains only the DPC and peptide. Unfortunately, these commands do not work since the micelle (and the peptide) are not in the box center. I have tried many others commands with -pbc as mol, res with no success. I have never had much success using multi-molecule groups for centering or other correction using trjconv. Centering on the peptide, i.e. trjconv -pbc mol -ur compact -center, should do the trick. I have never found -pbc nojump to work very well, for a reason that is still unknown to me. -Justin I used GMX version 4.0.7 Any advices would be helpful. Stefane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 6 Date: Fri, 20 Aug 2010 13:19:54 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intersting problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c6eb93a.6010...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed babu gokul wrote: dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard g_dist -dist -Justin E R Azhagiya singam -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 7 Date: Fri, 20 Aug 2010 21:55:40 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] force constants for umbrellla histograms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: daae7e83-e389-4dc8-9e38-517ab08d5...@rug.nl Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes The most important is that you have to put in trajectories that are equilibrated! You can mix as much force constant values you like but always equilibrated ... Then the lower the force constant the longer the simulation needs to be to reach equilibrium: larger conformational space accessible. I can also imagine that a too strong force constant might deform your molecules in a manner you should not. Then does it matter how many times you vary it, and how large ? In my sampling I have very good histograms up to 2 nm (force constant = 1000 kj/mol), above 2nm they are not. I feel I may have to use a force constant of 500 for the next 3 or 4 windows, and even less again (ca~ 50 kj/mol) beyond that. Cheers Gavin XAvier Periole wrote: On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Yes. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org
[gmx-users] How to center molecules in the box with trjconj ?
Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the peptide located at the micelle interface. Now I would like to plot some MD configs in a PDB format some configs where the micelle and the peptide are placed in the center of the box. To take into account the PBC and to obtain the PDB, for the last frame at 150 ns as I used trjconv with the following commands: 1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump -b 15 -e 15 -o traj_KTM17_DPC_0ns_noJump.pdb With non-SOL (DPC and peptide) as a group for output and where traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation 2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro -center -o traj_KTM17_DPC_0ns_noJump_center.pdb With DPC as a group for centering and System (DPC and peptide) as a group for output. the *.gro file contains only the DPC and peptide. Unfortunately, these commands do not work since the micelle (and the peptide) are not in the box center. I have tried many others commands with -pbc as mol, res with no success. I used GMX version 4.0.7 Any advices would be helpful. Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intrapeptide hbond existence map
Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 Thank you in advance for your help Stephane winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intrapeptide hbond existence map
Ok thank you all for your suggestions A bientot ABEL Stephane 175950 wrote: Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 The output file -hbn 4_Peptide_53A6_hbonds_400_500ns_index maps the donor-acceptor pairs to the plot. Find within that index file a directive that starts with hbonds that corresponds to all of the H-bonds that were found, and thus plotted. Red indicates the H-bond exists, white means it doesn't. As for occupancy, you'd probably have to script that to parse the .xpm file and calculate a percentage of frames for when the particular H-bond exists, or get lifetimes from g_hbond. -Justin .or to define smaller index groups, e.g. the NH- or CO-group of res 1, and get the number of hydrogen bonds as function of time from the -num output (default is hbnum.xvg). You would have to repeat this for all (reasonable combinations of) hbonding groups that you're interested in, which can result in maaany g_hbond executions. But if the number of groups are small, then it's certainly doable. It seems from your plot though, that scripted processing of the -hbm and -hbn output, as Justin suggests, is the way to go here. Make sure you're matching the index file to the xpm file in the right way! I've made mistakes in that area myself. Erik Thank you in advance for your help Stephane -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- Message: 5 Date: Thu, 11 Feb 2010 09:49:42 -0800 From: Lum Nforbi lumngwe...@gmail.com Subject: [gmx-users] Working with Reduced Units To: gmx-users@gromacs.org Message-ID: f7e1d8851002110949w126829c5y3f5f2859cef45...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi all, Please, can someone shed more light on how to set up reduced units in an .mdp file? I have tried to this but it does not work. I set epsilon, sigma and mass to 1 in my force field file as stated in section 2.3 of the manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon to get a temperature in reduced units with value 2.5. I also calculated the pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get a value of 0.0431 and included all of these in the .mdp file but this did not work for me in the mdrun. Is this the right way to set up reduced units in gromacs? Please, help me out. Thanks, Lum -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100211/890182c2/attachment-0001.html -- Message: 6 Date: Thu, 11 Feb 2010 18:40:10 + From: Rebeca Garc?a Fandi?o rega...@hotmail.com Subject: [gmx-users] different results in different machines To: gmx-users@gromacs.org Message-ID: bay142-w9ac927eb472e1c1568b58b7...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: comparation_neuron_ngs.pdf Type: application/pdf Size: 3110 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20100211/efa9e0c0/comparation_neuron_ngs.pdf -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 70, Issue 75 * winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] perl scripts to convert CHARMM ff in GROMACS
Hi GMXusers I am testing the parameters of CHARMM, it works fine for lipids and protein. This is a great job, thanks to the devellopers But i would like to add some new molecule for solvent (e.g. for TFE) The atom types of TFE are present in the ffcharmm27bon.itp available in latest port (c32b1_release_1.1.zip, dowloaded http://www.dbb.su.se/User:Bjelkmar/Ffcharmm), unfortunately several bonded parameters (for example F3-CF3, CF3-CT2x, etc..) are missing in ffcharmm27bon.itp file. So I need to convert the missing parameters into gromacs format. In website (URL:http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), I have found that several perl scripts exist for the conversion charmm-- gromacs. The archive is corrupted so, I cannot unpacked the directory to obtain the files. Where I can find these scripts Thanks in advance for your help Stephane winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] amidated C-terminus in the charmm ff port for gromacs
Hi everybody I am currently testing the CHARMM port for GROMACS pre4.1. I have downloaded the c32b1_release_1.1.zip file http://www.dbb.su.se/User:Bjelkmar/Ffcharmm (11:59, 23 Oct 2009). My protein protein have an acetylated N-terminus and amidated C-terminus. According to the CHARMM force field, these groups are considered as two residus named ACE and CT2, respectively. In the ffcharmm27.rtp, only the statement ACE, NMA are presents, where is the CT2 group in the file? Thank you in advance for your help. Stephane winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE : gmx-users Digest, Vol 69 , Issue 132
Thanks Justin Indeed, It worked !!! In french, one says: je ne dormirai pas idiot ce soir. Stéphane Thank you Roland for your response I have effectively downloaded from the http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version of gmx Unfortunately, the unpacked directory does not contain a configure file, I have only an configure.ac. So my question is: how to obtain a fully fonctional version of 4.1 without using git Thank you for your response Hi, there is currently no web-interface on the official git server. Thus repo.or.wz is probably the best solution. I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is up-to-date. Roland On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 stephane.a...@cea.frwrote: Hi all, For a future project, I would like to use gromacs for simulations with the CHARMM force field. I am aware that the CHARMM ff is not yet officially supported by gromacs, even if a paper about this port will be published soon. By reading the mailing list, I understand that a beta version of gmx4.1 is available for testing from the git depositary. I have tried to use git, but since I am behind a firewall, I cannot easily access to the depositary. I have tried to obtain a previous from http://repo.or.cz/w/gromacs.git through the master branch but I am not sure that the file downloaded was the latest version. Therefore, my question is how to obtain the latest version of pre gmx4.1 without using git ? Thank you for your help Stéphane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Message: 3 Date: Tue, 26 Jan 2010 14:00:00 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1 without git To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b5f3bb0.1000...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed Stephane Abel wrote: Thank you Roland for your response I have effectively downloaded from the http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version of gmx Unfortunately, the unpacked directory does not contain a configure file, I have only an configure.ac. So my question is: how to obtain a fully fonctional version of 4.1 without using git In the code you downloaded, there should be a script called bootstrap which you can execute to generate the configure file. -Justin Thank you for your response Hi, there is currently no web-interface on the official git server. Thus repo.or.wz is probably the best solution. I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is up-to-date. Roland On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 stephane.a...@cea.frwrote: Hi all, For a future project, I would like to use gromacs for simulations with the CHARMM force field. I am aware that the CHARMM ff is not yet officially supported by gromacs, even if a paper about this port will be published soon. By reading the mailing list, I understand that a beta version of gmx4.1 is available for testing from the git depositary. I have tried to use git, but since I am behind a firewall, I cannot easily access to the depositary. I have tried to obtain a previous from http://repo.or.cz/w/gromacs.git through the master branch but I am not sure that the file downloaded was the latest version. Therefore, my question is how to obtain the latest version of pre gmx4.1 without using git ? Thank you for your help Stéphane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 4 Date: Wed, 27 Jan 2010 08:09:47 +1100 From: Dallas B. Warren dallas.war...@pharm.monash.edu.au Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 89907ea1dcfb7548a431c13a270f9dd508fd8...@prk-exch-01.vcp.local
[gmx-users] Making Commands Non-Interactive
Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. Thank you again for your help winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] good Atom type in gromacs with the AMBER ff port
Hi gromacs users I have a newbie question about the atom type in gromacs. I would like to simulate a peptide with AMBER ff (ffamber03) in gromacs v.4.05 , so I have downloaded the ffamber files and followed the explanation given in Sorin's lab homepage. To neutralize my system i have added one CL- ion in the simulation box, but i am not sure it was good ion (in a other word the CL- ion compatible with the AMBER ff and not the default ion parameters). Here what i did - Added ions.itp file the following directive: #ifdef _FF_AMBER99 [ moleculetype ] ; molname nrexcl Cl- 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 amber99_301 CL- CL 1 -1 35.4530 #endif - Use the following command with genion genion_mpi -s ions.tpr -o beta-I-Ac-NH2_slv_AMBER_ions.gro -p topol.top -pname NA+ -nname CL- -nn 1 - genion passes correctly It is correct ? If not what is wrong ? Thanks in advance for your help. Stéphane ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
OK thank you Omer, for you response The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel stephane.a...@cea.fr wrote: tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.4 0.4 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090917/08293573/attachment-0001.html -- Message: 4 Date: Thu, 17 Sep 2009 01:39:15 -0700 From: Darrell Koskinen darre...@ece.ubc.ca Subject: [gmx-users] Periodic Boundary Conditions Location of Atoms NearBox Edges To: gmx-users@gromacs.org Message-ID: 4ab1f5b3.5060...@ece.ubc.ca Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet using periodic boundary conditions, should the box edges be located at the midpoints between the atomic bonds? Thanks. Darrell -- ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 65, Issue 97 * ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .pdb to .gro = the atoms are not conneced with VMD
Hi, VMD uses a heuristic method to know if some atoms are connected. Sometimes the method fails. To be sure (and see) the atoms are well connected in VMD, you need to provided a psf file with your pdb/gro in VMD. So in your case you gro files is correct (since you indicated that your system are correct). An alternative see you gro in other software in pymol to confirm. I hope it helps Stefane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] Date: dim. 05/10/2008 12:00 À: gmx-users@gromacs.org Objet : gmx-users Digest, Vol 54, Issue 18 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. PR after minimisation and PR of missing residues? (minnale ) 2. .pdb to .gro = the atoms are not conneced with VMD (Chih-Ying Lin) -- Message: 1 Date: 5 Oct 2008 05:26:52 - From: minnale [EMAIL PROTECTED] Subject: [gmx-users] PR after minimisation and PR of missing residues? To: gmx-users1 gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi all, I have two doubts on PR, may be these are trivial to you. 1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps are (a)Energy minimisation (b)Position restrain with force constant descendant manner and finally (c)production. Here my doubt that, is it require to do energy minimisation between PR and production? because after PR the system equilibrating properly if do one minimisation the structure looses bad contacts with low energy, am I right? 2.If my desire protein contain some missing residues(from PDB)rectified those residues by using INSIGHT-II. Later start simulations particularly at PR, is it require to keep restrain specifically on added missing residues or whole protein residues in .itp file? Any suggestions would be appreciated Thanks in advance. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081005/fff46f50/attachment-0001.html -- Message: 2 Date: Sun, 5 Oct 2008 01:53:36 -0700 From: Chih-Ying Lin [EMAIL PROTECTED] Subject: [gmx-users] .pdb to .gro = the atoms are not conneced with VMD To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi I make .pdb file to .gro file. With the VMD, the atoms are seen NOT conneced. Why? Is there any possible errors in my .gro file? Lin -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 54, Issue 18 * winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp file format, Resolved !!!
Hi Gromacs Users My Problem with do_dssp is resolved : my do_dssp was strangely corrupted. After recompilation it works well. Thank you for all people who helped me. See U soon on this mailing list Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fit the secondary structure time serie graph in page
Hi gromacs users When I use the xpm2ps utility to made a ps graphic of the secondary structure with my xpm file, the graph obtained is show in portrait orientation and by consequence trucated because the page width is to small. How to change the orientation of graph with xpm2ps (for example a landscape orientation) to fit the graph in one page ? Thanks for your response Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE : gmx-users Digest, Vol 45, Issue 36
Thanks Justin for your reply So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test. I obtained always the same error. Opening library file /applications/gromacs-3.2.1/share/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# Note that the pdb seems correct because the secondary structure can be obtained with Stride available in VMD. And my trajectory was made CHARMM ffield. is this a problem in this case Thank a lot My story with do_dssp As suggested David and others i rename my pdb file with the extension .pdb i used the following command ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb A menu appears, I choose the group 1 (protein) and i obtained the error message Opening library file /applications/gromacs-3.2.1/share/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# What iis the problem. I give below a part of my pdb file ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 ATOM 5 CACE 1 7.470 -8.140 -10.510 0.51 0.00 ATOM 6 OACE 1 7.594 -9.280 -10.074 -0.51 0.00 ATOM 7 NGLY 2 8.125 -7.096 -10.030 -0.47 0.00 ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 ATOM 12 CGLY 2 10.408 -6.734 -9.033 0.51 0.00 ATOM 13 OGLY 2 11.313 -7.365 -8.492 -0.51 0.00 ATOM 14 NASP 3 10.647 -5.532 -9.599 -0.47 0.00 ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 Thank you again for your kindly help Stefane ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. don't rename the .pdb file to .tpr. Just use .pdb -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Fri, 11 Jan 2008 09:30:47 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote: Mark Abraham [EMAIL PROTECTED] wrote Non-Protein serves well here. So a usual tc-grps line has Protein Non-Protein for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? I haven't read the code or found any mention in the manual, but I expect that src/share/top/aminoacids.dat contains the names of any amino acids, and thus implicitly defines these groups. Mark -- Message: 3 Date: Fri, 11 Jan 2008 09:24:40 +0800 From: xuji[EMAIL PROTECTED] Subject: [gmx-users] Asking help about PME To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=gb2312 Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel: +86-10-82627076 Fax:+86-10-62558065 [EMAIL PROTECTED] 2008-01-11 -- next part -- An HTML attachment was scrubbed... URL
[gmx-users] do_dssp file format
My story with do_dssp continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contentsPage=1 Boîte de réception As suggested David and others i rename my pdb file with the extension .pdb i used the following command ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb A menu appears, I choose the group 1 (protein) and i obtained the error message Opening library file /applications/gromacs-3.2.1/share/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# What iis the problem. I give below a part of my pdb file ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 ATOM 5 CACE 1 7.470 -8.140 -10.510 0.51 0.00 ATOM 6 OACE 1 7.594 -9.280 -10.074 -0.51 0.00 ATOM 7 NGLY 2 8.125 -7.096 -10.030 -0.47 0.00 ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 ATOM 12 CGLY 2 10.408 -6.734 -9.033 0.51 0.00 ATOM 13 OGLY 2 11.313 -7.365 -8.492 -0.51 0.00 ATOM 14 NASP 3 10.647 -5.532 -9.599 -0.47 0.00 ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 Thank you again for your kindly help Stefane ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. don't rename the .pdb file to .tpr. Just use .pdb -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Fri, 11 Jan 2008 09:30:47 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote: Mark Abraham [EMAIL PROTECTED] wrote Non-Protein serves well here. So a usual tc-grps line has Protein Non-Protein for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? I haven't read the code or found any mention in the manual, but I expect that src/share/top/aminoacids.dat contains the names of any amino acids, and thus implicitly defines these groups. Mark -- Message: 3 Date: Fri, 11 Jan 2008 09:24:40 +0800 From: xuji[EMAIL PROTECTED] Subject: [gmx-users] Asking help about PME To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=gb2312 Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel: +86-10-82627076 Fax:+86-10-62558065 [EMAIL PROTECTED] 2008-01-11 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/ca6a4e79/attachment-0001.html -- Message: 4 Date: Fri, 11 Jan 2008 13:10:11 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Asking help about PME To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text
[gmx-users] do_dssp file format
-11.574 -0.27 0.00 ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 ATOM 5 CACE 1 7.470 -8.140 -10.510 0.51 0.00 ATOM 6 OACE 1 7.594 -9.280 -10.074 -0.51 0.00 ATOM 7 NGLY 2 8.125 -7.096 -10.030 -0.47 0.00 ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 ATOM 12 CGLY 2 10.408 -6.734 -9.033 0.51 0.00 ATOM 13 OGLY 2 11.313 -7.365 -8.492 -0.51 0.00 ATOM 14 NASP 3 10.647 -5.532 -9.599 -0.47 0.00 ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 Thank you again for your kindly help Stefane ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. don't rename the .pdb file to .tpr. Just use .pdb -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Fri, 11 Jan 2008 09:30:47 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote: Mark Abraham [EMAIL PROTECTED] wrote Non-Protein serves well here. So a usual tc-grps line has Protein Non-Protein for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? I haven't read the code or found any mention in the manual, but I expect that src/share/top/aminoacids.dat contains the names of any amino acids, and thus implicitly defines these groups. Mark -- Message: 3 Date: Fri, 11 Jan 2008 09:24:40 +0800 From: xuji[EMAIL PROTECTED] Subject: [gmx-users] Asking help about PME To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=gb2312 Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel: +86-10-82627076 Fax:+86-10-62558065 [EMAIL PROTECTED] 2008-01-11 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/ca6a4e79/attachment-0001.html -- Message: 4 Date: Fri, 11 Jan 2008 13:10:11 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Asking help about PME To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=GB2312 xuji wrote: Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? From the gromacs source directory, try find * -name *pme* and grep -i pme src/*/*.c include/*.h include/*/*.h | grep -v -i development Mark -- Message: 5 Date: Fri, 11 Jan 2008 10:44:05 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] Asking help about PME To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL
[gmx-users] do_dssp file format
Hi gromacs users For my work I have performed some simulations of a protein in water with an other MD software not compatible with GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the with the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp tools Just run a 10-step MD simulation and generate one yourself. Or convert your other trajectories into .pdb format and use that as input to do_dssp. You do not necessarily need a .tpr file for do_dssp, see man do_dssp under the -s flag. Mark Thanks Mark for your suggestions but it is not working for me So i have tested an other approach with VMD to obtain the secondary structure time series for my protein. The ouput graph obtained is not pretty, so i would like to make for a paper a same graph that i found in some gromacs papers. For this i need to convert the output datas file of VMD to gromacs xpm file obtained with do_dssp with a script and convert it to ps with the xpm2ps tool. In gromacs documentation i can not find an exemple of xpm file generated with do_dssp. So it is possible to obtain from the gromacs users a small exemple of this file to see how the datas are arranged Thank you very much Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp file format
I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. Any help will be appreciate Stefane ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 ATOM 5 CACE 1 7.470 -8.140 -10.510 0.51 0.00 ATOM 6 OACE 1 7.594 -9.280 -10.074 -0.51 0.00 ATOM 7 NGLY 2 8.125 -7.096 -10.030 -0.47 0.00 ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 ATOM 12 CGLY 2 10.408 -6.734 -9.033 0.51 0.00 ATOM 13 OGLY 2 11.313 -7.365 -8.492 -0.51 0.00 ATOM 14 NASP 3 10.647 -5.532 -9.599 -0.47 0.00 ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 -- Message: 3 Date: Thu, 10 Jan 2008 13:03:30 -0500 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] do_dssp file format To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Quoting ABEL Stephane 175950 [EMAIL PROTECTED]: Hi gromacs users For my work I have performed some simulations of a protein in water with an other MD software not compatible with GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the with the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp tools Just run a 10-step MD simulation and generate one yourself. Or convert your other trajectories into .pdb format and use that as input to do_dssp. You do not necessarily need a .tpr file for do_dssp, see man do_dssp under the -s flag. Mark Thanks Mark for your suggestions but it is not working for me So i have tested an other approach with VMD to obtain the secondary structure time series for my protein. The ouput graph obtained is not pretty, so i would like to make for a paper a same graph that i found in some gromacs papers. For this i need to convert the output datas file of VMD to gromacs xpm file obtained with do_dssp with a script and convert it to ps with the xpm2ps tool. In gromacs documentation i can not find an exemple of xpm file generated with do_dssp. So it is possible to obtain from the gromacs users a small exemple of this file to see how the datas are arranged What exactly is not working? As in, what commands are you issuing? Did the MD fail, or the analysis of the trajectory? If you provide this type of information, we may be able to help you better. -Justin Thank you very much Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ -- Message: 4 Date: Thu, 10 Jan 2008 19:27:38 +0100 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Dihedral with parameters set to zero To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed van Bemmelen wrote: OK. Now I'm confused. What did you mean by the second part? Of course, when doing FEP with the B state different, you would gradually introduce a dihedral
[gmx-users] do_dssp file format
Hi gromacs users For my work I have performed some simulations of a protein in water with an other MD software not compatible with GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the do_dssp tool in GROMACS is made for this. This tools also plot the results in .xpm matrix file which can be convert with the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp tools Thank you very much in advance for you help Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
