Dr. Lemkul Thanks for your reply. However , I used npme = 0 and could then utilize 64 processes. I did a NPT equilibration with Berendsen thermostats / barostats and found after 5 ns the density to be 999 kg/cu m and average press = 0.4 bar. There was marginal drift. Are these artifacts or I need to equilibrate more ? I used AMBER99SB/TIP3P.
Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Mon, Nov 16, 2015 at 1:49 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: Problems with trjconv (Shantanu Maheshwari) > 2. Choosing LINCS setting / rcon for parallel mdrun (Agnivo Gosai) > 3. Re: Choosing LINCS setting / rcon for parallel mdrun > (Justin Lemkul) > 4. difference between entropic energy and free energy (Ming Tang) > 5. (no subject) (Mehriar Amininasab) > > > ---------- Forwarded message ---------- > From: Shantanu Maheshwari <shantanu...@gmail.com> > To: gmx-us...@gromacs.org > Cc: > Date: Mon, 16 Nov 2015 00:30:10 +0100 > Subject: Re: [gmx-users] Problems with trjconv > No it will not erase anything from .trr file. > > On Mon, Nov 16, 2015 at 12:21 AM, Mishelle Oña <samimi...@hotmail.com> > wrote: > > > Ok, but this erase the frame from my trajectory? because i don´t want to > > modify it. > > > > > Date: Mon, 16 Nov 2015 00:10:07 +0100 > > > From: shantanu...@gmail.com > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Problems with trjconv > > > > > > If you want to take out only one frame then you can use -dump option. > > > > > > trjconv -f trajcentrada.trr -dump 1646 -o 1646ps.gro > > > > > > On Sun, Nov 15, 2015 at 11:39 PM, Mishelle Oña <samimi...@hotmail.com> > > > wrote: > > > > > > > Yes, but I am not converting all the .trr file to gro I wanted to > take > > > > only one frame of the .trr and make it gro. That´s why my command is > > > > trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro > > > > if the command line above is wrong :( what is the command I should > use > > for > > > > taking out only one frame of a trajectory file in gro format > > > > Mishelle > > > > > > > > > From: mark.j.abra...@gmail.com > > > > > Date: Sun, 15 Nov 2015 22:06:38 +0000 > > > > > To: gmx-us...@gromacs.org > > > > > Subject: Re: [gmx-users] Problems with trjconv > > > > > > > > > > Hi, > > > > > > > > > > Your question had one-word answer, which I gave! :-) If the size > of > > your > > > > > files is worth thinking about, then converting them to gro format > is > > not > > > > a > > > > > great idea. > > > > > > > > > > Mark > > > > > > > > > > On Sun, 15 Nov 2015 21:56 Mishelle Oña <samimi...@hotmail.com> > > wrote: > > > > > > > > > > > Eh, I don´t understand what you mean, please explain me > > .Mishelle:) > > > > > > > > > > > > > From: mark.j.abra...@gmail.com > > > > > > > Date: Sun, 15 Nov 2015 19:28:47 +0000 > > > > > > > To: gmx-us...@gromacs.org > > > > > > > Subject: Re: [gmx-users] Problems with trjconv > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > Certainly. You do not want to convert non-trivial trajectories > to > > > > text > > > > > > > format. > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña < > > samimi...@hotmail.com> > > > > > > wrote: > > > > > > > > > > > > > > > well, I check and it is the same line of command. The biggest > > file > > > > has > > > > > > > > more weight than the .traj file and it is only a .gro file . > Is > > > > this > > > > > > > > posible? > > > > > > > > Mishelle > > > > > > > > > From: mark.j.abra...@gmail.com > > > > > > > > > Date: Sun, 15 Nov 2015 19:15:50 +0000 > > > > > > > > > To: gmx-us...@gromacs.org > > > > > > > > > Subject: Re: [gmx-users] Problems with trjconv > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > Either you didn't issue the same command (inspect your > > terminal > > > > > > history), > > > > > > > > > or the second operation didn't complete (for any number of > > > > reasons). > > > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña < > > > > samimi...@hotmail.com> > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > Hello, I have a question about trjconv. I have a .trr > file > > and > > > > I > > > > > > put > > > > > > > > the > > > > > > > > > > following line of command: trjconv -f trajcentrada.trr -b > > 1646 > > > > -e > > > > > > 1646 > > > > > > > > -o > > > > > > > > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I > > make > > > > the > > > > > > > > same and > > > > > > > > > > got a file of 506444 bytes. Do you know what is > > > > happening?Mishelle > > > > > > > > > > -- > > > > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > > before > > > > > > > > > > posting! > > > > > > > > > > > > > > > > > > > > * Can't post? 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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. > > > > -- > > 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. > > > > > > ---------- Forwarded message ---------- > From: Agnivo Gosai <agnivogromac...@gmail.com> > To: gmx-us...@gromacs.org > Cc: > Date: Sun, 15 Nov 2015 19:09:19 -0600 > Subject: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun > Dear Users, > > I tried to do a NVT run on a cluster with -np = 64. My system size is 12405 > atoms ( a protein in water ) > > I get the following error. > > ERROR. > > There is no domain decomposition for 56 nodes that is compatible with the > given box and a minimum cell size of 0.959375 nm > Change the number of nodes or mdrun option -rcon or -dds or your LINCS > settings > > 8 nodes were assigned for PME cal by mdrun > > This is the part of my NVT.mdp > > ; Bond parameters > continuation = no ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 1.4 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) > rvdw = 1.4 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.12 ; grid spacing for FFT > > I would still like to use 64 processes for the mdrun. Any suggestions > please. > > I am thinking of playing with -rcon. But I am not sure if it will affect > the accuracy of the simulation. > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > > > > ---------- Forwarded message ---------- > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Cc: > Date: Sun, 15 Nov 2015 20:14:27 -0500 > Subject: Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun > > > On 11/15/15 8:09 PM, Agnivo Gosai wrote: > >> Dear Users, >> >> I tried to do a NVT run on a cluster with -np = 64. My system size is >> 12405 >> atoms ( a protein in water ) >> >> I get the following error. >> >> ERROR. >> >> There is no domain decomposition for 56 nodes that is compatible with the >> given box and a minimum cell size of 0.959375 nm >> Change the number of nodes or mdrun option -rcon or -dds or your LINCS >> settings >> >> 8 nodes were assigned for PME cal by mdrun >> >> This is the part of my NVT.mdp >> >> ; Bond parameters >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist = 1.4 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.4 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.12 ; grid spacing for FFT >> >> I would still like to use 64 processes for the mdrun. Any suggestions >> please. >> >> > Your system is too small to decompose over 64 cores. One cannot > arbitrarily parallelize any system over any number of cores/nodes. > > -Justin > > I am thinking of playing with -rcon. But I am not sure if it will affect >> the accuracy of the simulation. >> >> Thanks & Regards >> Agnivo Gosai >> Grad Student, Iowa State University. >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > > ---------- Forwarded message ---------- > From: Ming Tang <m21.t...@qut.edu.au> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" < > gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: > Date: Mon, 16 Nov 2015 03:20:21 +0000 > Subject: [gmx-users] difference between entropic energy and free energy > Deer list, > > I am quite confused about the concept of entropic energy and free energy. > Could anybody help to tell me what is the difference between them? > > Thanks. > > > > ---------- Forwarded message ---------- > From: Mehriar Amininasab <aminina...@khayam.ut.ac.ir> > To: gmx-us...@gromacs.org > Cc: > Date: Mon, 16 Nov 2015 11:12:14 +0330 > Subject: [gmx-users] (no subject) > Dear gromacs users, > > Does anybody have an idea about the value of isothermal compressibility at > kbar pressures. > > yours, > Mehriar > > > -- > 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.