[gmx-users] Regarding coordinate mismatching.
Hi, I am running membrane dynamics. After giving this commnad grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr i am receiving the following errors: Generated 837 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (em.gro, 44494) does not match topology (topol.top, 43374) I am not getting how to rectify the error, number of coordinates in coordinate file em.gro(44494) doesnot match topology(topol.top, 43374). -- 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
Re: [gmx-users] LIGAND TOPOLOGY
On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote: Dear users, I have been trying to build la ligand topology of my ligand through the PRODRG web server. I have the following queries; According to Justin's important tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html i am lost on how to allocate equivalent charges to equivalent groups. I have read the recommended paper but seems still i have issues in allocating the correct charges to my groups. You'll have to be a lot more specific with what you're dealing with and what you're doing if you want to get any useful help. Secondly, its about how to determine which groups are encompassed by a charge group Attached find in my PRODRG input file. Attachments are not allowed on the mailing list. Someone out there help me in understanding this. Charge groups are used in the Gromos96 force fields and typically contain 2-4 atoms such that the group has an integral charge (generally -1, 0, or 1). Figures 1, 3, 4, and 5 of our paper (dx.doi.org/10.1021/ci100335w) show how to properly assign charge groups in molecules of increasing complexity. Our work should have encompassed almost all of the most commonly encountered functional groups. Other examples for well-known molecules can be found in the .rtp file for the force field. -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
Re: [gmx-users] Regarding coordinate mismatching.
On 8/27/13 5:59 AM, sanjay choubey wrote: Hi, I am running membrane dynamics. After giving this commnad grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr i am receiving the following errors: Generated 837 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (em.gro, 44494) does not match topology (topol.top, 43374) I am not getting how to rectify the error, number of coordinates in coordinate file em.gro(44494) doesnot match topology(topol.top, 43374). The answer is always bookkeeping. You haven't correctly accounted for some part of the system in the [molecules] directive. The difference is 1120, so it's not related to water molecules. You also say you're running a membrane system, but I see no evidence of lipids in the grompp output, but if indeed there are lipids, you likely had to remove some to accommodate the protein, but didn't remove them from the topology. -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: GPU version of Gromacs
Hi, Is it possible to calc the PME on the CUDA card? If it is possible, how can one do it? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010758.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] general question about molecule.rtp and pdb2gmx
Hi, a general question about writing molecule.rtp and how pdb2gmx treats it. I have a few atom types and a few atoms per each atom type. So a question - when I define interactions, say [ bonds ] can I define them by atomtype, rather that atom number?! *So like this:* [ B31 ] [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex oc15 hoz b_oc-h oc16 hoy b_oc-h oc17 hoy b_oc-h oc18 hoy b_oc-h oc19 hoy b_oc-h oc20 hoy b_oc-h oc21 hoy b_oc-h ac3 oc16a_oc-ac-h ac3 oc17a_oc-ac-h ac3 oc18a_oc-ac-h ac3 oc19a_oc-ac-h ac3 oc20a_oc-ac-h ac3 oc21a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h al1 o5 a_oc-ac-h al1 o4 a_oc-ac-h al1 o2 a_oc-ac-h al1 o7 a_oc-ac-h al1 o6 a_oc-ac-h al1 o3 a_oc-ac-h If I use the 1st I get .top that does not list interactions, just [ atoms ] and #include link to the FF. Is this still OK? Does it read the [ bonds ] interactions or just non bonded? Thank you, V -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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
Re: [gmx-users] Re: GPU version of Gromacs
No, that is not implemented. Roughly speaking, the CPU does the PME+bondeds while the GPU does the short-ranged interactions. Moving PME would only be worthwhile if there was a very weak CPU and it was cheap to do any necessary communication between GPUs. That day is not yet here :-) Mark On Tue, Aug 27, 2013 at 4:17 PM, grita cemilyi...@arcor.de wrote: Hi, Is it possible to calc the PME on the CUDA card? If it is possible, how can one do it? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010758.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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 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
Re: [gmx-users] general question about molecule.rtp and pdb2gmx
On 8/27/13 12:30 PM, Valentina wrote: Hi, a general question about writing molecule.rtp and how pdb2gmx treats it. I have a few atom types and a few atoms per each atom type. So a question - when I define interactions, say [ bonds ] can I define them by atomtype, rather that atom number?! *So like this:* [ B31 ] [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex oc15 hoz b_oc-h oc16 hoy b_oc-h oc17 hoy b_oc-h oc18 hoy b_oc-h oc19 hoy b_oc-h oc20 hoy b_oc-h oc21 hoy b_oc-h ac3 oc16a_oc-ac-h ac3 oc17a_oc-ac-h ac3 oc18a_oc-ac-h ac3 oc19a_oc-ac-h ac3 oc20a_oc-ac-h ac3 oc21a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h al1 o5 a_oc-ac-h al1 o4 a_oc-ac-h al1 o2 a_oc-ac-h al1 o7 a_oc-ac-h al1 o6 a_oc-ac-h al1 o3 a_oc-ac-h Defining by type is ambiguous. An .rtp requires that atom names be used to define connectivity. If I use the 1st I get .top that does not list interactions, just [ atoms ] and #include link to the FF. Is this still OK? Does it read the [ bonds ] interactions or just non bonded? No, it's not OK. In that case, you have no bonds at all, so your molecule would go flying apart. -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
Re: [gmx-users] general question about molecule.rtp and pdb2gmx
.rtp [bonds] requires atom names (because that's all that can be reliably deduced from the coordinate file input) .itp/.top [bonds] requires atom numbers (because prior sanity-ization is assumed) to look up the atom types to look up the interaction parameters ... and different force fields have slightly different details. Ain't life fun? Mark On Tue, Aug 27, 2013 at 6:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/27/13 12:30 PM, Valentina wrote: Hi, a general question about writing molecule.rtp and how pdb2gmx treats it. I have a few atom types and a few atoms per each atom type. So a question - when I define interactions, say [ bonds ] can I define them by atomtype, rather that atom number?! *So like this:* [ B31 ] [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex oc15 hoz b_oc-h oc16 hoy b_oc-h oc17 hoy b_oc-h oc18 hoy b_oc-h oc19 hoy b_oc-h oc20 hoy b_oc-h oc21 hoy b_oc-h ac3 oc16a_oc-ac-h ac3 oc17a_oc-ac-h ac3 oc18a_oc-ac-h ac3 oc19a_oc-ac-h ac3 oc20a_oc-ac-h ac3 oc21a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h al1 o5 a_oc-ac-h al1 o4 a_oc-ac-h al1 o2 a_oc-ac-h al1 o7 a_oc-ac-h al1 o6 a_oc-ac-h al1 o3 a_oc-ac-h Defining by type is ambiguous. An .rtp requires that atom names be used to define connectivity. If I use the 1st I get .top that does not list interactions, just [ atoms ] and #include link to the FF. Is this still OK? Does it read the [ bonds ] interactions or just non bonded? No, it's not OK. In that case, you have no bonds at all, so your molecule would go flying apart. -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 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: general question about molecule.rtp and pdb2gmx
Ok, thank you! I was hoping for an easier job. My system is anyhow flying apart - trying to spot a problem. Hence trying. One more question - [ pairs ] get automatically generated. But I don't need 1-4 LJ. So I can just remove them? Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010761.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] About script for free energy calculation
Dear Justin thank you for your Previous reply I am following your methane/water free energy tutorial I have Generated All .mdp files wiht Different LAMBDA value But When I Run job using Your Job.sh script in usr/local/gromacs4.6.2/bin I have Received the Following error ( I ma running this script by keepig in BIN directory) root@vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh ( the error is as follows) Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy .mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP Starting minimization for lambda = 0... ./job.sh: line 28: grompp_d: command not found ./job.sh: line 30: mdrun_d: command not found ./job.sh: line 41: grompp_d: command not found ./job.sh: line 45: mdrun_d: command not found Minimization complete. Starting constant volume equilibration... ./job.sh: line 60: grompp_d: command not found ./job.sh: line 62: mdrun_d: command not found Constant volume equilibration complete. Starting constant pressure equilibration... ./job.sh: line 77: grompp_d: command not found ./job.sh: line 79: mdrun_d: command not found Constant pressure equilibration complete. Starting production MD simulation... ./job.sh: line 93: grompp_d: command not found ./job.sh: line 95: mdrun_d: command not found Production MD complete. Ending. Job completed for lambda = 0 How to Solve it Thanks InAdvance -- 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
Re: [gmx-users] About script for free energy calculation
On Tue, Aug 27, 2013 at 7:05 PM, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin thank you for your Previous reply I am following your methane/water free energy tutorial I have Generated All .mdp files wiht Different LAMBDA value But When I Run job using Your Job.sh script in usr/local/gromacs4.6.2/bin I have Received the Following error ( I ma running this script by keepig in BIN directory) Don't. Your root privileges have just been revoked. :-) Learn to source GMXRC like the installation instructions say. Mark root@vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh ( the error is as follows) Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy .mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP Starting minimization for lambda = 0... ./job.sh: line 28: grompp_d: command not found ./job.sh: line 30: mdrun_d: command not found ./job.sh: line 41: grompp_d: command not found ./job.sh: line 45: mdrun_d: command not found Minimization complete. Starting constant volume equilibration... ./job.sh: line 60: grompp_d: command not found ./job.sh: line 62: mdrun_d: command not found Constant volume equilibration complete. Starting constant pressure equilibration... ./job.sh: line 77: grompp_d: command not found ./job.sh: line 79: mdrun_d: command not found Constant pressure equilibration complete. Starting production MD simulation... ./job.sh: line 93: grompp_d: command not found ./job.sh: line 95: mdrun_d: command not found Production MD complete. Ending. Job completed for lambda = 0 How to Solve it Thanks InAdvance -- 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
Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx
Yes, can remove. However, ability to remove don't depend on our desire, but depend on Force field set of rules. If molecule was parametrized with 1-4 LJ, it is not desirable to remove it. If it is in-house force field which ignore 1-4 LJ, then one can safely remove it. Sergey 27.08.2013, 20:42, Valentina valentina.erast...@durham.ac.uk: Ok, thank you! I was hoping for an easier job. My system is anyhow flying apart - trying to spot a problem. Hence trying. One more question - [ pairs ] get automatically generated. But I don't need 1-4 LJ. So I can just remove them? Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010761.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- Подлеца не будут носить крылья. Это общий закон птиц Кар-Карон -- 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: general question about molecule.rtp and pdb2gmx
Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent this output. Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010764.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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
Re: [gmx-users] Help with Error Message
Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.comwrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@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 http://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_Lists 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx
On 8/27/13 4:25 PM, Valentina wrote: Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent this output. No, that's not how gen-pairs works. There are many excellent explanations of how it works in the list archive, but suffice it to say it does not affect the appearance of pairs, instead it affects what parameters are applied (either looked up or generated). -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
Re: [gmx-users] Help with Error Message
I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file. On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.com wrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@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 http://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_Lists 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] Help with Error Message
Hi ..., You should have had a look at the topology file format in an earlier step. At the end is a listing of molecules. As it says in the tutorial, you replaced solvent by ions, and you have to make changes in the topology file to match that replacement. Open the file in an editor, have a look around, try to see where the number of solvent molecules is listed, and make the changes. Cheers, Tsjerk On Tue, Aug 27, 2013 at 10:41 PM, The One And Only chappybo...@gmail.comwrote: I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file. On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.com wrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@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 http://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_Lists 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list
Re: [gmx-users] Help with Error Message
What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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
Re: [gmx-users] Help with Error Message
a text editor On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.comwrote: What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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
Re: [gmx-users] Help with Error Message
An editor is a program to edit the text in a file: gedit, nano, vi, emacs, ... It'll be the equivalent of Windows' Notepad. Can you find a tutor around to help you out with the basic usage of Linux? It's always difficult to plunge into several different things at the same time, here 'using linux', 'performing simulations', and probably 'theory of molecular dynamics'. It helps to take one topic at a time, but that is not always possible. Cheers, T. On Tue, Aug 27, 2013 at 10:56 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: a text editor On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.com wrote: What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Rescale: Cloud simulation platform research grants
My name is Ilea Graedel, and I work at Rescale (www.rescale.com), a software company based in San Francisco, CA. Rescale provides a secure, web-based platform for engineers, scientists, and researchers to perform compute-intensive analyses in the cloud. We enable companies and academic institutions to run simulations faster then they can today. I'm writing to let you know that we have launched our first-ever Simulation Research Grant competition as part of the Rescale University Program (ReUP). Competition details are available herehttp://www.rescale.com/reup/reup-grants.pdf as well as below. With these grants, select researchers will have the opportunity to run their computing analyses and simulations for free on Rescale’s platform. Simulation Grant competition details: http://www.rescale.com/reup/reup-grants.pdf Feel free to email me (i...@rescale.com) if you have any questions. Regards, Ilea -- *Ilea Graedel* Manager, Business Development Rescale i...@rescale.comhttps://exchange.wpi.edu/owa/redir.aspx?C=95b409f15d4548af9dc3754fccb9708eURL=mailto%3asunny%40rescale.com +1 509 721 0629 This email is confidential and may be privileged. If you have received it in error, please notify us immediately and then delete it. Please do not copy it, disclose its contents or use it for any purpose. -- 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] Wrapping of protein molecules during simulation
Hi! I noticed that gromacs breaks molecules due to PBC during the output of trajectories. I understand that this can be fixed with trjconv. Is there any option in the parameter file to force gromacs to keep molecules whole? If not is it for efficiency purposes? Sorry, if this question might have been asked many times already, but I could not find an answer. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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
Re: [gmx-users] Wrapping of protein molecules during simulation
On 8/27/13 8:02 PM, Gianluca Interlandi wrote: Hi! I noticed that gromacs breaks molecules due to PBC during the output of trajectories. I understand that this can be fixed with trjconv. Is there any option in the parameter file to force gromacs to keep molecules whole? If not is it for efficiency purposes? Doing so serves no functional purpose, so there is no reason mdrun should waste time reconstructing molecules during the run (obtaining atomic positions from domains, reconstructing from the topology, etc). Many analysis tools don't even require whole molecules anyway; it's primarily a visualization convenience. -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] Gentle heating with implicit solvent
How important is it to do gentle heating (using simulated annealing) with GBSA? Often with explicit water it is enough to perform some equilibration with positional restraints. Would it be enough to do the same with implicit solvent? Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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
