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 ?
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 "Neighbor >> > > You 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 > > Thanks >> >> >> On 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 anything >>> else. >>> 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, >>>>> >>>>> Nitin >>>>>> >>>>>> >>>>>> >>>>>> On 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. >>>>>>>> >>>>>>>> LIE >>>>>>> assumes 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 LIE >>>>>>> >>>>>>> >>>>>>> >>>>>>>> If you evaluate the energies from a PME simulation, the result >>>>>>>> will >>>>>>>> be >>>>>>>> >>>>>>>> off. If you use plain cutoffs for the dynamics, the simulation >>>>>>> will >>>>>>> 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> >>>>>>> > >>>>>>> >>>>>>>> before >>>>>>>>> >>>>>>>> posting! >>>>>>> >>>>>>> * Please don't post (un)subscribe requests to the list. 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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. 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.**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> >>>>> <htt**p://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> >>>>> > >>>>> >>>>>> >>>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<**h**ttp://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> >>>>> >>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the www >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read >>>>> http://www.gromacs.org/******Support/Mailing_Lists<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. 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 <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> >>> <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/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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