Re: [gmx-users] gromacs cpu v/s gpu
Hi Gurunath, You have to run both simulations for (approximately) infinite time and compare the probability density functions to check whether the simulations are the same. Maybe running more simulations would also be a good idea. Here's something about simulations and statistics: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20341/full(sel-advertisement ;)) Cheers, Tsjerk On Wed, Jan 15, 2014 at 10:05 AM, Gurunath Katagi gurunath.kat...@gmail.com wrote: Hello everyone... I have done a MD simulation of peptide using gromacs 4.6.5 both on CPU based system (intel based) I have run the same simulation in the GPU based system (NVIDIA quadra ) to test whether i get the siulialr results. I have taken care into the necessary modifications in the mdp files lile cut-off scheme. But the results from the 50ns all-atom simulations with OPLS forcefield seems to be different . i.e the conformations that are resulting from the two runs are different... Can anybody suggest what other things are to be taken care apart from mdp file modifications while running on gpu, because the cpu based simulation run is giving the expected results. So now i need to utilize the gpu based system for further computing, i am just wondering how can reproduce the results in gpu based system...? Thank you Gurunath -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] PMF_Association
Dear All, I'm trying to examine the association of amino acid (gamma amino butric acid) in a non-polar solvent (trifluoroethanol). I calculated the PMF for three different concentrations of amino acid in solution along the distances between GABA molecules. Despite the fact that, increasing concentration of amino acid should lead to increasing association, we observe the most free energy changes in the most dilute solution (2M). Whereas the PMF for this solution doesn't have features of normal system with associated molecules, i mean contact minimum and ..., it is just increase dramatically at the first and then it remain constant. the other solutions which are more concentrated, have normal features but generally the free energy changes trend compare to concentration in weird. 0.019 molal solution of amino acid: delta G= -10.0 kcal.mol-1 0.601 molal : delta G=-1.0 kcal.mol-1 3.975 molal : delta G=-1.5 kcal.mol-1 now the question is: is there anything wrong with simulations? or i should just change the windows of examination? ( for example considering 8-20 angstrom in stead of 5-25 angstrom distances) I will be thankful if anybody can help me with this problem. -- 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] non-native contatcs
First define and calculate the native contacts (contacts which were present in native reference structure and exist for significant amount of time during simulation). Then you can identify the contacts which exist for significant amount of time but were not present in native reference structure (which may correspond to non-native contacts). On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal suhani.nag...@gmail.comwrote: Greetings I'm studying protein unfolding by CTMD and REMD simulations to capture the intermediate states. I want to calculate the non-native contacts formed during the intermediate state. Suggestions please Thanks Suhani Proteomics and Structural biology Lab CSIR-IGIB -- 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. -- *Thanks and Regards,Bipin Singh* -- 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] LR electrostatics in single point energy calculations
On 1/15/14, 7:14 AM, rajat desikan wrote: Hi All, I was wondering about the long range electrostatics while calculating single point energies. I did a cursory calculation for a protein in water (PME) and found that the LR electrostatic terms were zero. I know that the per-particle decomposition of the LR electrostatics is non trivial. I was wondering if there is a way to do it in Gromacs? Was the Coul-recip term actually zero, or were you looking at Coul-LR? The two terms mean very different things. -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] g_order (warning)
Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings: WARNING: distance between atoms 779 and 781 0.3 nm (1.626940). Index file might be corrupt. WARNING: distance between atoms 995 and 997 0.3 nm (0.397073). Index file might be corrupt. WARNING: distance between atoms 1157 and 1159 0.3 nm (1.788146). Index file might be corrupt. WARNING: distance between atoms 1265 and 1267 0.3 nm (0.828453). Index file might be corrupt. WARNING: distance between atoms 76 and 78 0.3 nm (0.747680). Index file might be corrupt. WARNING: distance between atoms 346 and 348 0.3 nm (3.898362). Index file might be corrupt. . . . After long time, deuter_sn1.xvg and order_sn1.xvg were obtained. How to remove these warnings? Are these warnings dangerous? Any help will highly appreciated. -- 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] pdb2gmx
Hello, I was under the impression that pdb2gmx was supposed to referance the force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem to be for me. To double check, I removed all force field parameters from forcefield.itp and pdb2gmx still ran and got the same result as before. How do I make pdb2gmx referance oplsaa.ff/forcefield.itp? Thank you! Jon -- 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] -norandom option removed?
Hello: I found that the -norandom option in genion was no longer in 4.6.5: genion -h Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt. Index file -oout.gro Output Structure file: gro g96 pdb etc. -p topol.top In/Out, Opt. Topology file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int0 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -seedint1993Seed for random number generator -concreal 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. These ions are added on top of those specified with -np/-nn or -conc. I am just wondering does it means the pme methods would be automatically for ion placement? thank you very much. Albert -- 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] LR electrostatics in single point energy calculations
Hi Justin, I used the following commands: mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro gmxdump_mpi -e ener.edr ener_readme And in the dump of the ener_readme file, I have the following terms: Coul-SR:Protein-Protein -6.62324e+05 LJ-SR:Protein-Protein -5.64854e+04 Coul-14:Protein-Protein 4.04345e+05 LJ-14:Protein-Protein 3.29438e+04 Coul-SR:Protein-POPC -1.97403e+03 LJ-SR:Protein-POPC -4.64531e+03 Coul-14:Protein-POPC 0.0e+00 LJ-14:Protein-POPC 0.0e+00 ...etc There is neither a Coul-recip nor a Coul-LR term. So, I was wondering about it. The Coul-recip is the reciprocal space term in a Ewald summation calculation, right? I want the total potential energy of the protein. How would I go about that? Thanks. On Wed, Jan 15, 2014 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/14, 7:14 AM, rajat desikan wrote: Hi All, I was wondering about the long range electrostatics while calculating single point energies. I did a cursory calculation for a protein in water (PME) and found that the LR electrostatic terms were zero. I know that the per-particle decomposition of the LR electrostatics is non trivial. I was wondering if there is a way to do it in Gromacs? Was the Coul-recip term actually zero, or were you looking at Coul-LR? The two terms mean very different things. -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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_order (warning)
On 1/15/14, 9:30 AM, shahab shariati wrote: Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings: WARNING: distance between atoms 779 and 781 0.3 nm (1.626940). Index file might be corrupt. WARNING: distance between atoms 995 and 997 0.3 nm (0.397073). Index file might be corrupt. WARNING: distance between atoms 1157 and 1159 0.3 nm (1.788146). Index file might be corrupt. WARNING: distance between atoms 1265 and 1267 0.3 nm (0.828453). Index file might be corrupt. WARNING: distance between atoms 76 and 78 0.3 nm (0.747680). Index file might be corrupt. WARNING: distance between atoms 346 and 348 0.3 nm (3.898362). Index file might be corrupt. . . . After long time, deuter_sn1.xvg and order_sn1.xvg were obtained. How to remove these warnings? Are these warnings dangerous? The warnings either indicate that the index groups were not constructed properly or that there is some wild behavior going on in the simulation. The printed atom numbers correspond to carbons n-1 and n+1 in the calculation of the order parameters. You can verify that the index groups are good by looking into the coordinate file to make sure they correspond to what you think they do. To verify that the trajectory is sensible, you'll have to visualize it, focusing on the potentially problematic atoms that are printed out. -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] -norandom option removed?
On 1/15/14, 10:52 AM, Albert wrote: Hello: I found that the -norandom option in genion was no longer in 4.6.5: genion -h Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt. Index file -oout.gro Output Structure file: gro g96 pdb etc. -p topol.top In/Out, Opt. Topology file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int0 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -seedint1993Seed for random number generator -concreal 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. These ions are added on top of those specified with -np/-nn or -conc. I am just wondering does it means the pme methods would be automatically for ion placement? Non-random placement never really worked, so it was removed as an option. Now, genion only places ions randomly. -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] non-native contatcs
Hi, I have never done this before. But is this a possibility? http://www.pymolwiki.org/index.php/Contact_map_visualizer On Wed, Jan 15, 2014 at 8:41 PM, bipin singh bipinel...@gmail.com wrote: Hello Dr. Justin, Yes, there is no in-built module in Gromacs to get the information about native contacts during the simulation, but I think it can be done using the following resources outside the Gromacs: http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html http://www.multiscalelab.org/utilities/RMSDTTNC On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/14, 7:11 AM, bipin singh wrote: First define and calculate the native contacts (contacts which were present in native reference structure and exist for significant amount of time during simulation). Then you can identify the contacts which exist for significant amount of time but were not present in native reference structure (which may correspond to non-native contacts). Can you actually do this within Gromacs, or outside software? I'd be curious to know. -Justin On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I'm studying protein unfolding by CTMD and REMD simulations to capture the intermediate states. I want to calculate the non-native contacts formed during the intermediate state. Suggestions please Thanks Suhani Proteomics and Structural biology Lab CSIR-IGIB -- 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. -- *Thanks and Regards,Bipin Singh* -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] scale tabulated non-bonded potentials?
Dear Gmx Users, Is there any way in Gromacs to scale tabulated potentials from energygrp_table (non-bonded)? Steven -- 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] trouble with gaia....
Hey Fra, if you have a few minutes could you maybe help me with some trouble I have with gaia? (session login seems to be corrupt / firefox cannot be started since it thinks I am still logged in seomwhere else) Best, Marc -- 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] trouble with gaia....
I am sorry this email was send to the wrong list. please disregard. Best, Marc Hoemberger On Wed, Jan 15, 2014 at 5:01 PM, Marc Hömberger hoe...@gmail.com wrote: Hey Fra, if you have a few minutes could you maybe help me with some trouble I have with gaia? (session login seems to be corrupt / firefox cannot be started since it thinks I am still logged in seomwhere else) Best, Marc -- 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] scale tabulated non-bonded potentials?
Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that the question you're asking? :-) Mark On Wed, Jan 15, 2014 at 8:02 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, Is there any way in Gromacs to scale tabulated potentials from energygrp_table (non-bonded)? Steven -- 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] LR electrostatics in single point energy calculations
On 1/15/14, 4:18 PM, rajat desikan wrote: Hi Justin, Thanks for the reply. So, must I use a separate .mdp file with infinite cutoffs for both vdw and coulomb to get all the LR interactions correctly? Can you give me specific pointers about the settings? Infinite cutoffs, zero steps, don't use constraints (so the coordinates don't change), then follow http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy. -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] About Tutorials
Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for REMD, Targeted MD , Constraint MD and Non Equilibrium MD as you develop the Tutorial for other Methods in your web page. Your Tutorial is so clear and understandable . So May I expect Tutorial for aforesaid Technique in nutshell manner? It will be highly helpful So i Humbly request you to Put Tutorial Thanks In Advance -- 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] About Tutorials
Dear Vidya sankar, I think this may help you with the REMD. Here's the link for the tutorial: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B This tutorial deals with REMD and was prepared by Mark Abraham for GROMACS 2013 conference. On Thu, Jan 16, 2014 at 11:31 AM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for REMD, Targeted MD , Constraint MD and Non Equilibrium MD as you develop the Tutorial for other Methods in your web page. Your Tutorial is so clear and understandable . So May I expect Tutorial for aforesaid Technique in nutshell manner? It will be highly helpful So i Humbly request you to Put Tutorial Thanks In Advance -- 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. -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- 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] gromacs bond restraints
How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures? Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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] g_helix segmentation fault grom-4.6.5
Software has bugs, unfortunately, and GROMACS tools particularly so. We are trying to improve the situation, but if a developer isn't using a tool, it doesn't get any love! Are you trying to say it doesn't work in 4.6.5? Mark On Jan 16, 2014 5:51 AM, tarak karmakar tarak20...@gmail.com wrote: Dear All, Bit confused with the g_helix utility in gromacs-4.6.5. I've simulated a membrane protein for 50 ns in gromacs-4.5.5. Now, I'm trying to analyze properties of each of the trans-membrane helices. g_helix in gromacs-4.5.5 seems not working properly and then I moved to gromacs-4.6.5 tools to analyze the trajectories. While doing so, make_ndx -f topol.tpr -o TM_1.ndx g_helix -s topol.tpr -f traj.xtc -n TM_1.ndx ... for few of the helices, it is showing ... There are 28 residues There are 26 complete backbone residues (from 2 to 27) nall=460 Reading file topol.tpr, VERSION 4.5.5 (single precision) helix from: 6 through 23 t=0.00 Back Off! I just backed up zconf.gro to ./#zconf.gro.4# Segmentation fault (core dumped) .. However, for other helices the similar protocol is working perfectly fine. It would be highly appreciated if anyone can comment or suggest on this problem. regards, Tarak -- 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] gromacs bond restraints
See chapter four for what is available, and tables in 5.5 for a summary of their use. Mark On Jan 16, 2014 5:11 AM, Neha Gandhi n.gandh...@gmail.com wrote: How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures? Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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.
