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 searching will be performed for every frame, unless nstlist is zero".. should i set nslist to zero in MDP file? 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.**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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