On 7/17/13 10:54 AM, Sainitin Donakonda wrote:
I started MD very recently dont have much experience you said i would need .tpr file which doesnot use PME ? how can i get that ?
By writing a new .mdp file that doesn't use PME. Please refer to previous discussions on this topic. People ask about LIE frequently, and for some reason there seems to be a rash of interest lately...
-Justin
Thanks, Nitin On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 7/17/13 10:43 AM, Sainitin Donakonda wrote:Ok..thanks...so i will use -rerun option in final production ..step..as follows...actually i ran 20 ns MD simulation so i used extend option to run everything in cluster in correct time #first 10 ns grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_10.tpr mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10 #extension for 10 more ns tpbconv -s MD_first10.tpr -extend 10000 -o md_extended_2.tpr mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi MD_first10.cpt -np 32 Can you please tell is this commands are appropriate for production run using -rerun option...in help manual it is mentioned that "NeighborYou will need a new .tpr file that does not use PME. Then, I would suggest concatenating the existing .xtc files to streamline the process. I also do not recall whether the -rerun option works in parallel, but in any case it is reasonably fast even in serial. Thus: mdrun -s newtpr.tpr -rerun full20ns.xtc searching will be performed for every frame, unless nstlist is zero"..should i set nslist to zero in MDP file?No. You want the neighbor list to be updated at every frame in the .xtc, otherwise you will miss interactions and the output will likely be flawed. -Justin ThanksOn Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 7/17/13 10:12 AM, Sainitin Donakonda wrote: Usually i collect data after final production run...after this i take.xtc file and analyze it using various gromacs tools .. And there you have it. LIE is just an analysis method like anythingelse. There is no purpose in my mind in reanalyzing nonbonded energies during equilibration. -Justin thanks,nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 7/17/13 9:21 AM, Sainitin Donakonda wrote: Hi justin,Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Which simulation stage do you normally use to collect data?-Justin Thanks, NitinOn Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 7/17/13 8:54 AM, Sainitin Donakonda wrote:Hi ,I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. The long-range mesh terms are not decomposable in a pairwise manner. LIEassumes that all of your interactions can be broken down from additive terms, and this is not the case with PME. and why we should use -rerun option beofre running LIEIf you evaluate the energies from a PME simulation, the result will be off. If you use plain cutoffs for the dynamics, the simulationwill probably be junk. So one solution is to run the simulation with PME to get reasonable dynamics, then post-process via mdrun -rerun while evaluating energies with plain cutoffs (which one would usually increase beyond normal values, IIRC, but I do not use LIE myself). -Justin -- ==============================********==================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.********edu <jalemkul@outerbanks.** umaryland.edu <jalemkul@outerbanks.**umaryla**nd.edu<http://umaryland.edu> <jalemkul@outerbanks.**umaryland.edu<jalem...@outerbanks.umaryland.edu>| (410) 706-7441 ==============================********==================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/********mailman/listinfo/gmx-users<http://lists.gromacs.org/******mailman/listinfo/gmx-users> <ht**tp://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users><htt**p://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> <h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users><htt**p://lists.gromacs.org/****mailman/**listinfo/gmx-users<http://lists.gromacs.org/**mailman/**listinfo/gmx-users><h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users><h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>* Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search<****h**ttp://www.gromacs.org/**** Support/** <http://www.gromacs.org/**Support/**><http://www.gromacs. **org/Support/** <http://www.gromacs.org/Support/**>> Mailing_Lists/Search<http://****www.gromacs.org/Support/**<http://www.gromacs.org/Support/**> Mailing_Lists/Search<http://**www.gromacs.org/Support/** Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>beforeposting!* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/******** Support/Mailing_Lists<http://www.gromacs.org/******Support/Mailing_Lists> <http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/****Support/Mailing_Lists><http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/**Support/**Mailing_Lists> <http:/**/www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists><http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/**Support/**Mailing_Lists><http:/**/www.gromacs.org/Support/****Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists><http:/**/www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>--==============================******====================Justin A. 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-- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
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