Dear users, Please let me know whether it is feasible and relevant or not if I use COM pulling for mechanical unfolding of proteins. More specifically, whether I can define the two group within the same molecule !!
On Wed, Aug 16, 2017 at 6:48 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Fwd: (Justin Lemkul) > 2. (Don't know if mail worked last time)Drift with > groups+tabulated potential. (spere...@us.es) > 3. how to make molecular model with both ion channel and lipid > bilayer? (Li, Tong) > 4. Re: how to make molecular model with both ion channel and > lipid bilayer? (h.aliza...@znu.ac.ir) > 5. Doing restart (?farial tavakoli? ?) > 6. npt simulation error (Mohammad Zahidul Hossain Khan) > 7. Re: npt simulation error (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Aug 2017 08:02:45 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: > Message-ID: <c2806875-ebe0-d575-e462-381c707ca...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 8/15/17 1:52 AM, saranya wrote: > > Hi, > > I have done protein-drug simulations for 100ns. While calculating the > hydrogen > > bond between the protein-drug complex I am getting only 2 hydrogen bonds. > > The number of H-bond formation is very low I have a question about is > there > > any influence of the drug in my protein? > To answer that, you need to do simulations of the apo protein and > compare whatever relevant structural metrics there are (not H-bonds, as > these tell you about the ligand-protein interactions but nothing about > the impact on the protein structure). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > > > ------------------------------ > > Message: 2 > Date: Tue, 15 Aug 2017 14:25:30 +0200 > From: spere...@us.es > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] (Don't know if mail worked last time)Drift with > groups+tabulated potential. > Message-ID: <4e579ca344c855cabbbbf935a5ebc...@us.es> > Content-Type: text/plain; charset=US-ASCII > > Dear GROMACS Community, > > First of all, if someone got this email twice, I am sorry. It is my > first post and I was not sure if it worked. > > I am trying to do a simulation using a tabulated potential which forces > me to use the group cut-off. I get a drift in the conserved quantity of > -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules > and a Na+ ion. I imagine that eventhough it will soon be deprecated the > group cutoff scheme still works correctly. I have tryed to change the > parameters without success and in any case the ones I use seem > reasonable (in my experience using other programs). The rdfs of the > system look normal so I ruled out topology problems. > > It seems that the problem is in the group cut-off since > when I change the tabulated potential for a regular vdw the problem > persists. I have followed the instructions of: > > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf > > to implement the tabulated potentials. > > Is this the kind of energy drift acceptable? I have pasted a copy .mdp > > Thanks for your help, > > Sergio Perez-Conesa > > integrator = md > dt = 0.001 > nsteps = 100000 > init-step = 0 > cutoff-scheme = group > nst-list = 1 > verlet-buffer-tolerance = 0.0005 > ns-type = grid > rlist = 1.3 > pbc = xyz > coulombtype = PME-switch > rcoulomb = 1. > rcoulomb-switch = 0.95 > pme-order = 4 > fourierspacing = 0.1 > ewald-rtol = 1.e-5 > vdwtype = user > rvdw = 1.0 > DispCorr = No > tcoupl = v-rescale > tc-grps = System > ;nsttcouple = 1 > tau-t = ref-t = 300.0 > constraints = all-angles > constraint-algorithm = LINCS > lincs_iter = 1 > lincs_order = 4 > energygrps = NA OW > energygrp_table = NA OW > comm-mode = linear > > ------------------------------ > > Message: 3 > Date: Tue, 15 Aug 2017 15:09:27 +0000 > From: "Li, Tong" <ton...@udel.edu> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] how to make molecular model with both ion channel > and lipid bilayer? > Message-ID: <a58e2d39d21544f2a8a14ff6e9eff...@udel.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > I am trying to make a model of ion channel with cell membrane. Is there a > specific software to make this? I mean just the coordination file. VMD can > generate the membrane automatically, I can find the 'pdb' files of ion > channels, but I have no idea how to combine them. > > Thanks all, > Tong > > > ------------------------------ > > Message: 4 > Date: Tue, 15 Aug 2017 16:49:43 +0000 > From: h.aliza...@znu.ac.ir > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how to make molecular model with both ion > channel and lipid bilayer? > Message-ID: <d39070d67bb0c37d48b5c650a2939...@mail.znu.ac.ir> > Content-Type: text/plain; charset="utf-8" > > Charmm-gui.org could help you. > Bests, > Hadi > On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: > Dear all, > > I am trying to make a model of ion channel with cell membrane. Is there a > specific software to make this? I mean just the coordination file. VMD can > generate the membrane automatically, I can find the 'pdb' files of ion > channels, but I have no idea how to combine them. > > Thanks all, > Tong > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List (http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List) before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ( > http://www.gromacs.org/Support/Mailing_Lists) > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users ( > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users) or > send a mail to gmx-users-requ...@gromacs.org (mailto:gmx-users-request@ > gromacs.org). > > > ------------------------------ > > Message: 5 > Date: Tue, 15 Aug 2017 22:46:14 +0000 (UTC) > From: ?farial tavakoli? ? <farial.tavak...@ymail.com> > To: Discussion List for GROMACS Users <gmx-us...@gromacs.org> > Subject: [gmx-users] Doing restart > Message-ID: <1962486576.3101166.1502837174...@mail.yahoo.com> > Content-Type: text/plain; charset=UTF-8 > > #yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted > {margin-left:0 !important;border-left:1px #715FFA solid > !important;padding-left:1ex !important;background-color:white;} Dear gmx > users > I stoped my md simulation and now i want to restart it. > I use gromacs 2016.3? and issued this command to perform md:Gmx grompp -f > md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx > mdrun -deffnm md_0_1 > To restart simulation i issuedGmx mdrun -s md_0_1.tpr ?-cpi md_0_1.cpt > -appendBut faced to an error: > Fatal error: > File appending requested, but 2 of the 3 output files are not present or > are > named differently. For safety reasons, GROMACS-2016 and later only allows > file > appending to be used when all files have the same names as they had in the > original run. Checkpointing is merely intended for plain continuation of > runs. > For safety reasons you must specify all file names (e.g. with -deffnm), and > all these files must match the names used in the run prior to checkpointing > since we will append to them by default. If the files are not available, > you > can add the -noappend flag to mdrun and write separate new parts. For mere > concatenation of files, you should use the gmx trjcat tool instead. > > i refered to google but i couldnt understand well what should i type > exactly. would you please help me to restart my md simulation? > Thanks in advanceFarial > > > Sent from Yahoo Mail for iPhone > > > ------------------------------ > > Message: 6 > Date: Tue, 15 Aug 2017 18:14:49 -0700 > From: Mohammad Zahidul Hossain Khan <za.par...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] npt simulation error > Message-ID: > <CAAdBV7bGg0ZPm-R9nO8tagfPorV15h1bFp=FR30+Sf1gRW= > z...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Sir > > I am trying to simulate protein_ligand complex using epsilon = 4 and it is > giving the below error > > *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension x* > > I have no idea how to solve this problem > -- > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* > * Skype: parash.khan2* > *Cell: +12085967165* > > ------------------------------ > > Message: 7 > Date: Tue, 15 Aug 2017 21:18:14 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] npt simulation error > Message-ID: <dd482641-ce0a-a873-f7f9-13b04f752...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > > Dear Sir > > > > I am trying to simulate protein_ligand complex using epsilon = 4 and it > is > > giving the below error > > > > What is epsilon = 4? > > > *2 particles communicated to PME rank 4 are more than 2/3 times the > cut-off > > out of the domain decomposition cell of their charge group in dimension > x* > > > > I have no idea how to solve this problem > > > > Have you Googled it, or gone to the GROMACS error page, where lots of > advice > lives? ;) > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 160, Issue 74 > ****************************************************** > -- Nabajyoti Goswami Research Associate Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- 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.
