[gmx-users] acpype error
I installed acpype to generate the necessary files of ligand.if I use this command: "Acpype -i ligand.mol2 -c user" I will get following message:"ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'" Please guide meThanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hydrophobic interactions and electrostatic interactions between the protein chains
Hi dear GROMACS usersI want to calculate hydrophobic interactions and electrostatic interactions between the protein chains using gromacs trajectory . Please guide me.Thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] hydrophobic interactions and electrostatic interactions between the protein chains
Hi dear GROMACS usersI want to calculate hydrophobic interactions and electrostatic interactions between the protein chains using gromacs trajectory . Please guide me.Thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] potential energy
Hi all GMX usersI did MD simulation under NPT ensembel. I evaluated potential energy during energy minimization, equilibration, and productionMD steps. The plot of potential energy indicates the nice, steady convergence of potentialenergy during energy minimization step. The first equilibration phase has been conductedunder an NVT ensemble. The temperature of the system quickly has been reachedthe target value (300 K) during this step. The potential energy has been alsoincreased quickly and then reached to steady state. Is the system in its minimum potential energy in this step? The potential energy has been almost constantduring the second equilibration phase and production MD. These steps performed under NPT ensemble. Did MD sinualtion perform appropriately? please guide me.Thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] one protein and 4 ligands
Dear justinThank you so muchI did MD simulation on some protein-ligand complexes but I don't know that I must use one mol2 file for 4 ligands or separate mol2 files for each ligand. I want to calculate free energy value for this complex by GMXPBSA script. Must free energy value be calculated for 4 lignads simultaneously? or I can calculate free energy value for each lignad individually.Thank you for kindness Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] one protein and 4 ligands
I want to do MD simulation on a protein-ligand complex. the protein includes 4 chains and the ligands are ASP amino acid. I want to use Amber topologies from acpype for generating necessary files for ligands. please guide me to do this work correctly. Can I use GMXPBSA script to obtain free energy value for the studied protein-ligand complex.Thank you so muchBest wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] average pressure
Hi all GMX usereI have a large system composed of three protein chains. I simulated it in a triclinic box. I used Parrinello-Rahman with tau-p=2 in NPT equilibration step for 1000 ps. When I checked average pressure in this step, I find an average pressure of ~ 22 bar, rather than 1 bar. I extended this step for 3000 ps but I get similar value for average pressure. Which parameter must I change to get better average pressure?Please guide meThank you so much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] average pressure
Hi all GMX usereI have a large system composed of three protein chains. I simulated it in a triclinic box. I used Parrinello-Rahman with tau-p=2 in NPT equilibration step. When I checked average pressure in this step, I find an average pressure of ~ 22 bar, rather than 1 bar. Which parameter must I change to get better average pressure?Please guide meThank you so mich -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] an error related to Gromacs version
Hi all GMX usersI did MD simulation by Gromacs 5.1.2 and I want to calculate free energy by GMXPBSA script. This script don't work correctly with Gromacs 5.1.2 so I have to done free energy calculation by Gromacs 5.0.7. If I do this calculation I will get an error related to Gromacs version. Is there any way to solve this problem?Please help me thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] metal ions in equilibration step
Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step, should I consider protein,ligand and calcium ions as one single entity (for tc_grps option)? or should I consider these calcium as the part of ions in sol-ions group?ThanksBest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Index is larger than the number of atoms in the trajectory file
Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation. If I remove calcium ions, I will get following error in the first step of MMPBSA calculation:Fatal error: Index[1673] 1676 is larger than the number of atoms in the trajectory file (1675). There is a mismatch in the contents of your -f, -s and/or -n files.How can I solve this problem. please guide me Thank you so much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Calcium ions in GMXPBSA approch
Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation. I have two question, please guide me:1- must I remove calcium ions in free energy calculation?2- If I remove calcium ions, I will get following error in the first step of MMPBSA calculation:Fatal error: Index[1673] 1676 is larger than the number of atoms in the trajectory file (1675). There is a mismatch in the contents of your -f, -s and/or -n files.Thank you so much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: modelling of calcium ions
Hi Thank you for your answersI want to change ffnonbonded.itp file for calcium ions. Have nm and KJ/mol units been used for sigma and epsilon values in this file, respectively? I ask this question to ensure. On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: I thank you for your answer.I want to change ffnonbonded.itp file for calcium ions. Have nm and KJ/mol units been used for sigma and epsilon values in this file, respectively? I ask this question to ensure. Thank you so much Best wishes On Sunday, February 5, 2017 9:29 PM, Christopher Neale <chris.ne...@alum.utoronto.ca> wrote: The things you'll have to be most careful of include whether the calcium ion parameters you choose can get the correct coordination states (as I recall, Calcium's coordination can be quite variable experimentally, in contrast to something like magnesium, which has a more strict coordination number). You can check this possibly by putting a calcium ion in water and integrating the RDF over the first shell, etc (or, obviously reading the literature about simulations with those ca2+ parameters). In addition, you might have to think about getting the right chi rotamers of asn and gln if they assist coordination (they are not always correct in crystal structures) and protonation states of coordinating side chains. For example, I am not sure if His can help to coordinate calcium, but if it can then you'll want to have the right tautomer (protonation on the epsilon vs delta nitrogen atom), etc. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 05 February 2017 11:18:10 To: gmx-us...@gromacs.org; Mahboobeh Eslami Subject: Re: [gmx-users] modelling of calcium ions On 2/5/17 4:18 AM, Mahboobeh Eslami wrote: > Hi all GMX usersI hope you are wellI want to simulate a protein-ligand > complex. There are two calcium ions in the crystallographic structure of > protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I > use these parameter for modelling of calcium ions.? Please guide me.ThanksBest > Ca2+ is already present in every force field in GROMACS. pdb2gmx should handle it out of the box as long as the residue is named appropriately. If you have (good) reason to change any aspects of the parameters, you'll have to alter ffnonbonded.itp to change the attributes of the corresponding atom type. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] modelling of calcium ions
On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: Hi Thank you for your answersI want to change ffnonbonded.itp file for calcium ions. Have nm and KJ/mol units been used for sigma and epsilon values in this file, respectively? I ask this question to ensure.Thank you so much Best wishes On Sunday, February 5, 2017 9:29 PM, Christopher Neale <chris.ne...@alum.utoronto.ca> wrote: The things you'll have to be most careful of include whether the calcium ion parameters you choose can get the correct coordination states (as I recall, Calcium's coordination can be quite variable experimentally, in contrast to something like magnesium, which has a more strict coordination number). You can check this possibly by putting a calcium ion in water and integrating the RDF over the first shell, etc (or, obviously reading the literature about simulations with those ca2+ parameters). In addition, you might have to think about getting the right chi rotamers of asn and gln if they assist coordination (they are not always correct in crystal structures) and protonation states of coordinating side chains. For example, I am not sure if His can help to coordinate calcium, but if it can then you'll want to have the right tautomer (protonation on the epsilon vs delta nitrogen atom), etc. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 05 February 2017 11:18:10 To: gmx-us...@gromacs.org; Mahboobeh Eslami Subject: Re: [gmx-users] modelling of calcium ions On 2/5/17 4:18 AM, Mahboobeh Eslami wrote: > Hi all GMX usersI hope you are wellI want to simulate a protein-ligand > complex. There are two calcium ions in the crystallographic structure of > protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I > use these parameter for modelling of calcium ions.? Please guide me.ThanksBest > Ca2+ is already present in every force field in GROMACS. pdb2gmx should handle it out of the box as long as the residue is named appropriately. If you have (good) reason to change any aspects of the parameters, you'll have to alter ffnonbonded.itp to change the attributes of the corresponding atom type. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] modelling of calcium ions
Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. There are two calcium ions in the crystallographic structure of protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I use these parameter for modelling of calcium ions.? Please guide me.ThanksBest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi dear GROMACS usersI hope you are well I performed a md simulation. When simulation was finished, I moved our files to another place. Unfortunately, trajectory files (.trr and .xtc files) were damaged. Can I produce new trajectory files form checkpoint file (.cpt)?Please guide meThank you so muchBest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] refinement of homology-based protein structure
On Wednesday, October 5, 2016 8:11 PM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: Hi I hope you are very well I designed one protein by Homology modelling approach. I want to use this protein as receptor in docking process. I think that, before docking process, initial designed protein must be refined by MD simulation. How much time should this simulation be done for refinement of homology-based protein structure. What parameters should be monitored to ensure that the time simulation is sufficient. thanks for your help best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] evaluation of influence of pH on the stability of protein
On Monday, August 29, 2016 11:40 PM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] evaluation of influence of pH on the stability of protein
Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: The average number of H-bonds
On Saturday, July 9, 2016 7:19 PM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: Hi GMX usersI have performed MD simulation on Protein-DNA complex for 100 ns.I want to calculate the average number of H-bonds over time. I studied a paper that the average number of H-bonds over time had been calculated for protein and DNA separately but I don't know that how this parameter has been calculated. How is this parameter calculated?thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] use of two index group simultaneously
hi all GMX usersI want to use of mindist command for two index groups that have already been created. how do I use of two index group simultaneously. when in use " -n index1.ndx -n index2.ndx" I get following error:fatal error:double command line argument -n -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] RMSD plot of the backbone atoms
hi GMX usersi have done MD simulation for a protein-protein complex. i want to get RMSD plot of the backbone atoms for one of the protein chain. how do i prepare index file?thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Restart the interrupted program
hi allI performed 20 ns MD simulation, but in the middle of the simulation time, my run was interrupted twice and I restarted it. Now, despite the end of the simulation time and all the steps, the program not be interrupted? It is very important to me. Please help me. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: protein-DNA complex
On Monday, February 29, 2016 12:55 PM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: dear Justinthanks for your answerI have another question. Which of the following items is better in mdp file for the equilibration and MD production steps? tc-grps = Protein-DNASOL-ION or tc-grps = Protein DNA SOL-ION Sincerely thank youbest On Saturday, February 27, 2016 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/27/16 3:03 AM, Mahboobeh Eslami wrote: > hi all I want to do molecular dynamics simulations on protein-DNA complex. > should the simulation of protein-DNA complex be done like the > protein-protein complex? or is it better to select different force field for > protein and DNA separately in MD simulation of protein-DNA? How is simulated > protein-DNA complex? Thanks so much for your help. > It's just like simulating any other molecule-in-water system, be it a single or multiple proteins. You shouldn't choose different force fields, because mixing and matching is generally a very (very very very) bad idea. All modern biomolecular force fields support proteins, DNA, and more. Read up on the quality of each before moving on; for instance, the AMBER implementations in GROMACS rely on very outdated AMBER nucleic acid force fields, and should be replaced with the more recent parameter sets. I believe some of these are available on the GROMACS user contributions page, but the validation issues, AFAIK, were never resolved, so check carefully... -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein-DNA complex
hi all I want to do molecular dynamics simulations on protein-DNA complex. should the simulation of protein-DNA complex be done like the protein-protein complex? or is it better to select different force field for protein and DNA separately in MD simulation of protein-DNA? How is simulated protein-DNA complex? Thanks so much for your help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-protein interaction
Thanks so much for your help On Thursday, January 28, 2016 8:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 1/28/16 10:58 AM, Mahboobeh Eslami wrote: > hi all I have used the HEX software for docking two protein.I want to do >molecular dynamics simulations on the obtained complex from docking process. >should the simulation of protein-protein complex be done like the >protein-ligand complex or the protein in water simulation? How is simulated >protein-protein complex? It is no different than simulating a single protein. pdb2gmx will give you topologies for each chain, then proceed with solvation, etc. like anything else. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein-protein interaction
hi all I have used the HEX software for docking two protein.I want to do molecular dynamics simulations on the obtained complex from docking process. should the simulation of protein-protein complex be done like the protein-ligand complex or the protein in water simulation? How is simulated protein-protein complex? Thanks so much for your help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
Thanks my friendsI checked new trajectory by gmxcheck and get following text: Reading frame 0 time 7000.000 # Atoms 8383 Precision 0.001 (nm) Reading frame 5000 time 17000.000 Item #frames Timestep (ps) Step 5501 2 Time 5501 2 Lambda 0 Coords 5501 2 Velocities 0 Forces 0 Box 5501 2 Reading frame is 5000 but desired frames are 5500 frame. I'm confused.best On Saturday, April 25, 2015 5:42 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Mahboobeh,I recommend checking the created trajectories with gmx check. CheersJames On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang m21.t...@qut.edu.au wrote: Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - frame 3500 time 17000.000 - frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjconv for cutting the trajectory in small subtrajectories
hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - frame 3500 time 17000.000 - frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
hi dear mingYes. Sorry, I've used the following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -b 1 -e 17000
but I do not get the desired result.best
On Saturday, April 25, 2015 5:09 PM, Ming Tang m21.t...@qut.edu.au wrote:
#yiv1199526006 -- .yiv1199526006EmailQuote
{margin-left:1pt;padding-left:4pt;border-left:#80 2px solid;}#yiv1199526006
Hi，-e is end frame， -b is the start one.
Sent from my Huawei Mobile
Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote:
hi GMx user I simulated protein-ligand comolex with gromacs. total simulation
time is 20ns. when I use trjconv for cutting the trajectory in small
subtrajectories from 1ps to 17000ps by following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000
I see following text in terminal window;
Reading frame 0 time 1.000
Precision of md-nopbc.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
- frame 3500 time 17000.000 - frame 3000 time 16000.000
I think the generated trajectory is incomplete because saved frame is
incomplete. please guide me.
Many thanks tobest
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[gmx-users] fatal error while running gmxpbsa0.sh
hi Dear GMX users, I use of GMXPBSA tool 2.1, I want to calculate free energy for protein-ligand complex. I used the following parameters in my mdp file in MD simulation step: cut-off scheme = Verlet but when I run gmxpbsa0.sh, I get following error: Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet please help meI sincerely thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] interaction between ligand and protein
I sincerely thank you for your answer. Is the RMSD values of system be monitored or the RMSD values of only protein or ligand. Which RMSD do I check? On Sunday, November 30, 2014 8:34 PM, Onur Tuna onurt...@hacettepe.edu.tr wrote: Dear Mahboobeh, You mean from which frame you should choose? If so, first look at RMSD values in order to make sure your system is stable. If it is stable you can choose the last configuration. Best, Onur On 30 Nov 2014, at 18:57, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. Which configuration should be chosen for the study of interactions between proteins and ligands? Thank you for your kindness -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] interaction between ligand and protein
dear justinI want to report final interactions in the form of an image. Is it wrong? Is it possible to create an image of all the frames? I sincerely thank you On Sunday, November 30, 2014 8:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/30/14 11:57 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. Which configuration should be chosen for the study of interactions between proteins and ligands? Why choose one configuration when you have a whole trajectory's worth of data? That's the principal advantage of the simulation - you study dynamic behavior. A single snapshot rarely, if ever, tells the whole story. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] do_dssp
hi GMX usersi use gromacs4.6.5 for protein-ligand complex simulationi wasn to study second structure of my protein for 20ns simulation. i used DSSP . I copied dssp file in /local/usr/bin and use following commandschmod +x dssp./dsspwhen i use following command:do_dssp -f md.xtc -s md.tpr -o md-ss.xpmi get following error:Failed to execute command: Try specifying your dssp version with the -ver option. when i use -ver option, i get the same message.please help methanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] minimization for final configuration
hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: minimization for final configuration
dear Justin thanks for your replyThe plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value?Sincerely.On Tuesday, September 30, 2014 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. An average structure might be totally unphysical. Energy minimization of an unphysical structure leads you to something that is probably useless. I'd suggest doing clustering if you're interested in the predominant conformation(s) during a certain time period of the simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi GMX users what command should I use to obtain the average structure in pdb format for two nanosecond of the end of simulation.Thank you sincerely for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein-ligand complex by gromacs
hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked all of the input files and the steps , but I did not understand why this happened. Please help me . Thank you for your kindness -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] calculate the ∆SASA for free energy calculation
dear justin Thank you for your guidance. I've done it. When I use the g_sas command, and asked me the following question: Select a group for calculation of surface and a group for output I do not know what groups should be selected. Sincerely. On Monday, August 25, 2014 5:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/25/14, 5:23 AM, Mahboobeh Eslami wrote: i want to calculate free energy by LIE method. I need to calculate the∆SASA. i need to calculate SASA in protein-ligand complex simulation and SASA in ligand -water simulation. Please guide me how I calculate it. Run two simulations (complex and ligand in solution) and use g_sas/gmx sasa. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] calculate the ∆SASA for free energy calculation
dear justin I did the following steps. Is it true or not? protein and ligand are merged by make_ndx in protein-ligand complex simulation. I've used the following command: g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: protein_ligand select a group: protein_ligand I have SASA in bound state. SASA in ligand -water simulation is calculated by Previous command but select a group: ligand select a group: ligand I have SASA in free state. ∆SASA is the difference between these two stages. Please tell me your opinion about these steps Thank you for your guidance. On Monday, August 25, 2014 6:40 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear justin Thank you for your guidance. I've done it. When I use the g_sas command, and asked me the following question: Select a group for calculation of surface and a group for output I do not know what groups should be selected. Sincerely. On Monday, August 25, 2014 5:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/25/14, 5:23 AM, Mahboobeh Eslami wrote: i want to calculate free energy by LIE method. I need to calculate the∆SASA. i need to calculate SASA in protein-ligand complex simulation and SASA in ligand -water simulation. Please guide me how I calculate it. Run two simulations (complex and ligand in solution) and use g_sas/gmx sasa. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the average value of the pressure
Dear Gromacs experts i simulated protein ligand complex by gromacs 4.6.3 I get following results for pressure in npt equilibration step: Energy Average Err.Est. RMSD Tot-Drift --- Pressure 1.58469 0.47 77.8738 2.403 (bar) but in production MD, i get following result Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.648902 0.13 70.6382 0.354397 (bar) are the average values of the pressure reasonable. I'm confused. Please help me. Thank you sincerely -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the average value of the pressure
dear justin Thank you sincerely for your good advice Good luck On Wednesday, July 16, 2014 8:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/14, 11:18 AM, Mahboobeh Eslami wrote: Dear Gromacs experts i simulated protein ligand complex by gromacs 4.6.3 I get following results for pressure in npt equilibration step: Energy Average Err.Est. RMSD Tot-Drift --- Pressure 1.58469 0.47 77.8738 2.403 (bar) but in production MD, i get following result Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.648902 0.13 70.6382 0.354397 (bar) are the average values of the pressure reasonable. I'm confused. Please help me. Yes. See http://www.gromacs.org/Documentation/Terminology/Pressure and the million or so previous posts on this same topic. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LIE method
hi dear justin A few months ago I asked you a question about LIE method. According to your guide, i wrote a new .mdp file that didn't use PME (I used RF) and used following command for protein-ligand complex and ligand-sol simulations: mdrun -s newtpr.tpr -rerun full20ns.xtc then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. But the obtained free energy has great difference with the experimental value. You told me that i must re-calculate energies from PME systems, then i must take the difference of the energies from another system where the same correction hasn't been applied. Please explain this. How do I do it? I have urgent need to calculate the free energy. Thank you sincerely On Monday, January 13, 2014 5:22 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/12/14, 5:18 PM, Mahboobeh Eslami wrote: dear Justin thanks a lot I use Amber03 force field and TIP3P water model for my system. following options are used in first my mdp file: nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 I have following questions. if possible, please answer them. 1) are these options good for LIE method? do LIE method need especial options? Run settings like these are dependent upon the force field. LIE is simply a post-processing technique. 2) I saw following advice in gmx forum save a lot of frames to get reasonably accurate numbers (http://gromacs.5086.x6.nabble.com/PME-td4450969.html) do you have especial comment for frame saving? No insight there. I am not familiar with the details of what was proposed in that post. As far as I know, most people do not attempt to re-figure energies like that; they simply re-process using RF or long cutoffs (RF is better). 3) I use *coulombtype = *cutoff and rcoulomb = 1.0 in new mdp file for rerun energies. are these options good or not? No, plain cutoffs are very inaccurate. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LIE method
hi dear justin A few months ago I asked you a question about LIE method. According to your guide, i wrote a new .mdp file that didn't use PME (I used RF) and used following command for protein-ligand complex? and ligand-sol simulations: ?mdrun -s newtpr.tpr -rerun full20ns.xtc ?then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. But the obtained free energy has great difference with the experimental value. You told me that i must re-calculate energies from? PME systems, then i must take the difference of the energies from another system where the same correction hasn't been applied. Please explain this. How do I do it? I have urgent need to calculate the free energy. Thank you sincerely -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
hi GMX users i want to use Reaction-Field for coulombtype in mdp file. i dont know that what parameters must be added in mdp file. i saw the following parameters in some of mdp fiels: ; Method for doing electrostatics coulombtype = reaction-field rcoulomb-switch = 0 rcoulomb = 0.80 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 epsilon-rf = 0 What values can rcoulomb-switch take? what values are the best for epsilon-r and epsilon-rf? Thank you sincerely. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Reaction-Field for coulombtype
On Tuesday, May 27, 2014 4:42 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i want to use Reaction-Field for coulombtype in mdp file. i dont know that what parameters must be added in mdp file. i saw the following parameters in some of mdp fiels: ; Method for doing electrostatics coulombtype = reaction-field rcoulomb-switch = 0 rcoulomb = 0.80 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 epsilon-rf = 0 What values can rcoulomb-switch take? what values are the best for epsilon-r and epsilon-rf? Thank you sincerely. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT simulation stage
dear Mr.alizadeh thanks for your reply the repeatability of average pressure is my problem. average pressure isn't repeatability when i repeat NPT simulation stage many times, simulation results are very different for the pressure average. my system is protein-ligand complex. How long do you think is enough for the NPT stage? Regards On , Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear Mr.alizadeh thanks for your reply my problem hasn't good repeatability. when i repeat NPT simulation stage many times, simulation results are very different for the pressure average. my system is protein-ligand complex. How long do you think is enough for the NPT stage? Regards On Monday, April 28, 2014 12:48 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mahboobeh, I do not know what component your system includes. However, based on my experiences, the fluctuation of pressure is high especially for small and incompressible systems. Besides, you should increase your simulation time. You should not expect that the pressure can converge exactly to the pressure you want. I think(I do not know details of your simulations) pressure fluctuation is natural, of course not for short simulations, the average pressure for equilibriated systems is important. --dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl?? = Parrinello-Rahman? Pcoupltype?? = Isotropic?? tau_p??? = 0.5??? compressibility? = 4.5e-5?? ref_p??? = 1.0??? refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p? but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage? many times,? simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations.? It can fluctuate dramatically.? Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT simulation stage
dear Mr.alizadeh thanks for your reply my problem hasn't good repeatability. when i repeat NPT simulation stage many times, simulation results are very different for the pressure average. my system is protein-ligand complex. How long do you think is enough for the NPT stage? Regards On Monday, April 28, 2014 12:48 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mahboobeh, I do not know what component your system includes. However, based on my experiences, the fluctuation of pressure is high especially for small and incompressible systems. Besides, you should increase your simulation time. You should not expect that the pressure can converge exactly to the pressure you want. I think(I do not know details of your simulations) pressure fluctuation is natural, of course not for short simulations, the average pressure for equilibriated systems is important. --dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl?? = Parrinello-Rahman? Pcoupltype?? = Isotropic?? tau_p??? = 0.5??? compressibility? = 4.5e-5?? ref_p??? = 1.0??? refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p? but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage? many times,? simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations.? It can fluctuate dramatically.? Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT simulation stage
dear justin Thank you sincerely. I wish you the best. Regards mahboobeh On Monday, April 28, 2014 2:48 PM, Justin Lemkul jalem...@vt.edu wrote: Please keep the discussion on the list. I can see from the other posts that providing this information to everyone likely would have been helpful. On 4/28/14, 2:44 AM, Mahboobeh Eslami wrote: dear justin I sent you the actual results for the repeated three times NPT stage: Energy Average Err.Est. RMSD Tot-Drift --- Pressure -1.86895 1.7 74.4741 8.46672 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Pressure -1.01376 3.1 76.8484 0.464786 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.251751 3.7 80.9027 -1.89681 (bar) if i change tau_p for the second NPT stage to 6 i will get following result: Energy Average Err.Est. RMSD Tot-Drift --- Pressure 1.20898 1.9 78.1862 0.931217 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Pressure -0.514578 1.8 78.6336 -2.57617 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Pressure 5.67055 1.9 80.5453 2.32409 (bar) Increasing tau_p relaxes the stringency of the barostat; I would expect the results to be worse when doing so. The bigger point here is that none of this looks anomalous to me. You're doing short NPT (100 ps), during which the pressure is unlikely to relax fully. More importantly, look at the actual numbers: -2 ± 75, -1 ± 77, 0.2 ± 81. Are any of these significantly different from the target value of 1 or do they differ significantly from one another? I'd say no. Pressure is ill-defined and subject to very large fluctuations. I wouldn't call any of this cause for concern. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT simulation stage
dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations. It can fluctuate dramatically. Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] parameters of ligand for force field OPLS
hi GMX users can i use acpype program for ligand preparation in simulation by gromacs? how can i produce the parameters of ligand for force field OPLS? thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] AMBER03 force field for protein-ligand complex
hi GMX users i want to use AMBER03 force field for protein-ligand complex simulation. can i use antechamber for the particle charges of the ligand or i must to use b3lyp/cc-pVTZ calculation in an implicit solvent model? thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] leapfrog does not yet support Nose-Hoover chains
hi GMX users if i use Nose-Hoover thermostat for ligand-protein simulation, i will get following note: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1. my protein has 1 chain. is the note important for ligand-protein simulation? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Adding Ions step
hi GMX users The output of pdb2gmx told me that the protein-ligand complex has a net charge of 0(zero) but at the last line of my[ atoms ] directive in topol.top;qtot 2.749e-06 . be read . 1)What does this mean? 2) if my system has a net charge of 0(zero),must iadd ions to my system for neutralize? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex
dear justin I thank you for your friendly guide Can I assume some of torsion steady and don't change them for getting results better of docking ? can i reduce rotatable bonds for my ligand in docking process then do MD simulation? if i reduce rotatable bonds, i will get much better results of docking. Your sincerely On Friday, January 17, 2014 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/17/14, 10:23 AM, Mahboobeh Eslami wrote: dear justin Some articles mentioned that the protein simulation in water before docking can improve the docking results. Do you think that this is true? Yes. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex
dear justin i have another question Can the increasing of MD simulation time improve docking results? can the increasing of MD simulation time create the experimental conformation of the ligand in the active site of the protein or close to it? I'm sorry if my question has problem grammar I am sorry for asking so many questions. thanks a lot On Friday, January 17, 2014 11:04 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear justin I sincerely thank you Can I use flexible receptor in docking process and then do the MD simulation? In this case, will the coordinates of the protein in MD simulation be changed? best wishes for you On Thursday, January 16, 2014 11:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/16/14, 9:51 AM, Mahboobeh Eslami wrote: hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose. This pose was almost close to the experimental structure, but not much. i run 10ns simulation but the simulation results were not close to the experimental results, especially conformation of the ligand in the active site of the protein. You have two potential problems, either the ligand topology or its initial pose. Run a simulation of the experimental complex, and if the ligand's position deviates similarly, then your topology is of poor quality. If it is reasonable, then your docked pose is of insufficient quality (almost close...but not much does not inspire confidence). -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex
dear justin thanks a lot if i use flexible receptor in docking process, must i change the coordinates of the protein as initial configuration in the MD simulation? Sincerely On Friday, January 17, 2014 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/17/14, 3:15 AM, Mahboobeh Eslami wrote: dear justin i have another question Can the increasing of MD simulation time improve docking results? can the increasing of MD simulation time create the experimental conformation of the ligand in the active site of the protein or close to it? Possibly, but the original point stands - if the initial pose is very poor or the topology incorrect, more running time usually just means more wasted time. You need to establish whether or not your starting conditions are reasonable. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex
dear justin Some articles mentioned that the protein simulation in water before docking can improve the docking results. Do you think that this is true? Thank you for your helpful answers On Friday, January 17, 2014 6:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/17/14, 9:54 AM, Mahboobeh Eslami wrote: dear justin thanks a lot if i use flexible receptor in docking process, must i change the coordinates of the protein as initial configuration in the MD simulation? No, that doesn't make any sense and only serves to add another variable into an already unclear situation. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein-ligand complex
hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose. This pose was almost close to the experimental structure, but not much. i run 10ns simulation but the simulation results were not close to the experimental results, especially conformation of the ligand in the active site of the protein. I sincerely request your help. thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex
dear justin I sincerely thank you Can I use flexible receptor in docking process and then do the MD simulation? In this case, will the coordinates of the protein in MD simulation be changed? best wishes for you On Thursday, January 16, 2014 11:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/16/14, 9:51 AM, Mahboobeh Eslami wrote: hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose. This pose was almost close to the experimental structure, but not much. i run 10ns simulation but the simulation results were not close to the experimental results, especially conformation of the ligand in the active site of the protein. You have two potential problems, either the ligand topology or its initial pose. Run a simulation of the experimental complex, and if the ligand's position deviates similarly, then your topology is of poor quality. If it is reasonable, then your docked pose is of insufficient quality (almost close...but not much does not inspire confidence). -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LIE method
dear justin I sincerely thank you for your answer my questions I saw the following description for tpbconv command in the gromacs manual: by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method. I do not know how to use this command.I think that this command is used only for charged ligand. is this correct? Thanks and best wishes On Sunday, January 12, 2014 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/12/14, 12:03 AM, Mahboobeh Eslami wrote: dear Justin thanks for your reply is the rerun energies needed only for protein ligand complex? do the ligand in water simulation need the rerun energies? Both. It wouldn't make sense to re-calculate energies from one PME system, then try to take the difference of the energies from another system where the same correction hasn't been applied. -Justin thanks a lot On Sunday, January 12, 2014 1:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote: hi dear GMX users I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free energy by LIE method so I simulated ligand in water in the same conditions. I used PME and full periodic boundary conditions in my simulations so I wrote a new .mdp file that didn't use PME (I used cut off) and used following command for protein-ligand complex simulation: mdrun -s newtpr.tpr -rerun full20ns.xtc then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. are these steps sufficient. is the stage or another commandnecessary? If the protein-ligand simulation was done with PME as well, then you need to get the rerun energies, as well. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LIE method
dear Justin thanks a lot I use Amber03 force field and TIP3P water model for my system. following options are used in first my mdp file: nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 I have following questions. if possible, please answer them. 1) are these options good for LIE method? do LIE method need especial options? 2) I saw following advice in gmx forum save a lot of frames to get reasonably accurate numbers (http://gromacs.5086.x6.nabble.com/PME-td4450969.html) do you have especial comment for frame saving? 3) I use coulombtype = cutoff and rcoulomb = 1.0 in new mdp file for rerun energies. are these options good or not? Thanks for your of kindness. On Sunday, January 12, 2014 8:36 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear justin I sincerely thank you for your answer my questions I saw the following description for tpbconv command in the gromacs manual: by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method. I do not know how to use this command.I think that this command is used only for charged ligand. is this correct? Thanks and best wishes On Sunday, January 12, 2014 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/12/14, 12:03 AM, Mahboobeh Eslami wrote: dear Justin thanks for your reply is the rerun energies needed only for protein ligand complex? do the ligand in water simulation need the rerun energies? Both. It wouldn't make sense to re-calculate energies from one PME system, then try to take the difference of the energies from another system where the same correction hasn't been applied. -Justin thanks a lot On Sunday, January 12, 2014 1:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote: hi dear GMX users I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free energy by LIE method so I simulated ligand in water in the same conditions. I used PME and full periodic boundary conditions in my simulations so I wrote a new .mdp file that didn't use PME (I used cut off) and used following command for protein-ligand complex simulation: mdrun -s newtpr.tpr -rerun full20ns.xtc then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. are these steps sufficient. is the stage or another commandnecessary? If the protein-ligand simulation was done with PME as well, then you need to get the rerun energies, as well. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbeforeposting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersorsend a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LIE method
dear Justin thanks for your reply is the rerun energies needed only for protein ligand complex? do the ligand in water simulation need the rerun energies? thanks a lot On Sunday, January 12, 2014 1:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote: hi dear GMX users I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free energy by LIE method so I simulated ligand in water in the same conditions. I used PME and full periodic boundary conditions in my simulations so I wrote a new .mdp file that didn't use PME (I used cut off) and used following command for protein-ligand complex simulation: mdrun -s newtpr.tpr -rerun full20ns.xtc then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. are these steps sufficient. is the stage or another commandnecessary? If the protein-ligand simulation was done with PME as well, then you need to get the rerun energies, as well. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Berendsen and Parrinello-Rahman
hi all my friends i am studying protein-ligand complex by gromacs 4.6.3 i see followingText in gromacs site: Berendsen is often the best algorithm for equilibration, because it is the most robust to the volume changes that might be expected during equilibration. However it does not generate the proper thermodynamic ensemble, so once the volume has stabilized, another method should be used to equilibrate into the right ensemble. can i use two NPT equilibration and can i use Berendsen andParrinello-Rahman for them? thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pressure coupling in NPT equilibration step
hi GMX user please help me i want to study protein ligand complex by gromacs4.6.3. i repaired my protein by MODELER and docked my ligand by AUTODOCK software. i use amber99sb-ildn force field. after Energy Minimization i use following option forTemperature coupling in NVT equilibration step: ; Temperature coupling tcoupl = v-rescale ; Couple temperature to external heat bath according to velocity re-scale method tc-grps = Protein_UNK NA_SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; Coupling time constant, controlling strength of coupling ref_t = 300 300 ; Temperature of heat bath then i use following option for Pressure coupling in NPT equilibration step ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT Pcoupltype = Isotropic ; uniform scaling of box vectors tau_p = 0.5 ; time constant, in ps compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ref_p = 1.0 ; reference pressure, in bar refcoord_scaling = com i obtain temperature average 299.63 for NVT step bu i obtain pressure average 1.35 for NPT stepI tried Various Thermostats and Barostatsbut i don’t get good pressure averageClose to 1bar. please help me thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: Pressure coupling in NPT equilibration step
On Monday, December 16, 2013 11:12 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX user please help me i want to study protein ligand complex by gromacs4.6.3. i repaired my protein by MODELER and docked my ligand by AUTODOCK software. i use amber99sb-ildn force field. after Energy Minimization i use following option forTemperature coupling in NVT equilibration step: ; Temperature coupling tcoupl = v-rescale ; Couple temperature to external heat bath according to velocity re-scale method tc-grps = Protein_UNK NA_SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; Coupling time constant, controlling strength of coupling ref_t = 300 300 ; Temperature of heat bath then i use following option for Pressure coupling in NPT equilibration step ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT Pcoupltype = Isotropic ; uniform scaling of box vectors tau_p = 0.5 ; time constant, in ps compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ref_p = 1.0 ; reference pressure, in bar refcoord_scaling = com i obtain temperature average 299.63 for NVT step bu i obtain pressure average 1.35 for NPT stepI tried Various Thermostats and Barostats but i don’t get good pressure average Close to 1bar. please help me thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: the crashed run
thanks for your reply please suggest the best command for restart a crashed run. i use following command mdrun -v -deffnm md -cpi md is this command good or not? thanks On Sunday, December 8, 2013 2:18 PM, jkrie...@mrc-lmb.cam.ac.uk jkrie...@mrc-lmb.cam.ac.uk wrote: _prev.cpt might be ok. I think it writes those in case the current cpt causes problems On 8 Dec 2013, at 09:57, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i use gromacs 4.6.3 double precision for protein ligand complex during the 20 ns. my run crashed, I'm not sure that restart my run from cpt file or run a new production. is the result of started again run a reliable like a non crashed run. thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fw: the crashed run
thanks for your reply Have a Great Day On Monday, December 9, 2013 1:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/13 6:59 AM, Mahboobeh Eslami wrote: thanks for your reply please suggest the best command for restart a crashed run. i use following command mdrun -v -deffnm md -cpi md is this command good or not? If the desired .cpt file is md.cpt, then mdrun -deffnm md -cpi suffices. If you need a previous .cpt file (i.e. md_prev.cpt), then you must specify its name explicitly. Depending on why the run crashed, simply restarting may not be worthwhile. If the crash was due to the system blowing up, it is a waste of time and you should investigate the crash. If it was a hardware failure, disk error, etc. then continuing from a checkpoint is fine. -Justin thanks On Sunday, December 8, 2013 2:18 PM, jkrie...@mrc-lmb.cam.ac.uk jkrie...@mrc-lmb.cam.ac.uk wrote: _prev.cpt might be ok. I think it writes those in case the current cpt causes problems On 8 Dec 2013, at 09:57, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i use gromacs 4.6.3 double precision for protein ligand complex during the 20 ns. my run crashed, I'm not sure that restart my run from cpt file or run a new production. is the result of started again run a reliable like a non crashed run. thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] charge correction in topology file from PRODRG
dear justin thanks for your help On Monday, December 9, 2013 1:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/13 6:18 AM, XAvier Periole wrote: For gromos ff you can also use the ATB server. From Alan Mark on Brisbane. It combine typography and non-bonded parameters all at once. It is not perfect but pretty good. shameless self-promotion For those wondering about some potential implications of topology errors and how to start going about fixing them, as well as an overview of some common QM calculations one can do to try to calculate charges for new groups: http://pubs.acs.org/doi/abs/10.1021/ci100335w /shameless self-promotion -Justin On Dec 8, 2013, at 8:27, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi all my friends I use PRODRG and antechmber for building topology and coordinate files for my ligand separately. i want to use GROMOS force field so i must to use the topology from PRODRG server. can i use the topology of antechamber for charge correction in topology fiel from PRODRG . In general, are special principlesessential for charge correction in topology file from PRODRG thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] charge correction in topology file from PRODRG
hi all my friends I use PRODRG and antechmber for building topology and coordinate files for my ligand separately. i want to use GROMOS force field so i must to use the topology from PRODRG server. can i use the topology of antechamber for charge correction in topology fiel from PRODRG . In general, are special principlesessential for charge correction in topology file from PRODRG thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field for prodrg server
dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned that PRODRG is used for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field? On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: hi dear Justin You've written the following context in your tutorial: Force field (GROMOS96.1/GROMOS87): GROMOS96.1 refers to the first version of the GROMOS96 force field, 43A1. GROMOS87 refers to the (outdated!) GROMOS87 force field. Choose GROMOS96.1 to get 43A1 parameters for our ligand but I don't see the option for Select the force field in PRODRG server PRODRG is now hosted by a company, so I don't know what sorts of changes they have introduced. There is no more force field selection, so it's a black box, I suppose. Given that you probably have to re-write the topology anyway, it probably doesn't matter much except for a few atom types that may be different between the force fields. ATB is probably a better option; I think its output is generally much more reliable than PRODRG. I'll probably revise the tutorial at some point, but the use of PRODRG to get a flawed topology is a good teaching tool. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gen_seed
Hi Dear Gmx Users what is the different between gen_seed= -1 and gen_seed=173529? what is the best for NVTequilibration? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ATB SERVER
hi my friends I use ATB server for my ligands. which are itp and pdb file used for ligands in md simulation by gromacs. thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GMX_THREAD_MPI=ON does not exis
hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs but i get following error: CMake Error: The source directory /home/elahe/.local/share/Trash/files/gromacs-4.2.6.3/build/GMX_THREAD_MPI=ON does not exist. Specify --help for usage, or press the help button on the CMake GUI. thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX_THREAD_MPI=ON does not exis
Thank you for your help What command do I use to use 8 cores Good luck On Friday, November 29, 2013 7:22 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs but i get following error: CMake Error: The source directory /home/elahe/.local/share/Trash/files/gromacs-4.2.6.3/build/GMX_THREAD_MPI=ON does not exist. Specify --help for usage, or press the help button on the CMake GUI. thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.
i want to install gromacs4.6.3 on 8 core. i use following command: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs is it correct? What command do I use to use 8 cores? which valid command line argument do i use by mdrun_mpi_d for 8 cores. thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun_mpi_d
hi i installed openmpi and i set -DGMX_MPI=ON in cmake command. are these casesenough? thanks On Friday, November 29, 2013 7:59 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Eslami, Gromacs 4.6.3 can automatically take up all the cores. If you want to run gromacs across the nodes. Then you need to compile using MPI. Detailed instruction is available here http://www.gromacs.org/Documentation/Installation_Instructions. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Nov 29, 2013 at 3:27 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: Hi everybody i install gromacs 4.6.3 double precision and parallel what is the best correct command for mdrun_mpi_d on single machine with multiple processors (core=8) thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] calculate velocity autocorrelation function
dear mohsen, dear mark thanks a lot On Wednesday, November 27, 2013 5:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Mahboobeh I think you just need to use g_velacc along with -h option after simulating your system. Besides you can have a look at manual, required options in mdp file have been mentioned. And maybe looking at some articles which have done this before using Gromacs! Best Mohsen On Wed, Nov 27, 2013 at 5:24 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear justin Do I need a special option in the mdp file. thanks a lot On Wednesday, November 27, 2013 4:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/27/13 1:16 AM, Mahboobeh Eslami wrote: hi Dear Gmx Users please help me i want to calculate velocity autocorrelation function by gromacs but I do not know exactly what is needed. Please Help me, please g_velacc -h -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
hi Dear Gmx Users i want to study the changing of velocity in production stage, do i set gen_vel= yes, gen_temp = 300 and gen_seed = -1 in all mdp file for Equilibration and production or only in production stage? should I setother options in the mdp file. Thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
