Re: [gmx-users] DPOSRES not working
I cant say I fancy one who wants make money on knowing what on other peoples mind, but that does not mean you are the same! :) I think this worked out, but what the "bug" may be, that after doing 5 simulations twice, each time the confout.gro is something different from the confout.gro that came out afterwards from using gmx trjconv maybe something irrelated and related to linux command line/rights etc? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 3:02:10 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 8:52 AM, Sergio Manzetti wrote: > Hey Justin , you sound like Mark Zuckerberg :) I don't know whether that's good or bad... > Here is the command I used: > > gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 -dump 1 is easier than using -b and -e, FYI. > > and it gives the write gro with DNA in the box as it should be. So then things worked, yes? > This confout.gro is not the same as came out from the GMX run, at the same > moment as the TRJ and XTC came In what way? Why does this lead you to believe that your restraints aren't working? The questions I asked before are more diagnostic of whether or not things are functioning. Dumping a (non-PBC-corrected) frame and looking at another one (PBC corrected, albeit perhaps not in the best way) does not say anything about whether or not the algorithms are working. -Justin > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > > > > From: "Justin Lemkul" <jalem...@vt.edu> > To: "gmx-users" <gmx-us...@gromacs.org> > Sent: Thursday, September 7, 2017 2:55:05 PM > Subject: Re: [gmx-users] DPOSRES not working > > On 9/7/17 8:45 AM, Sergio Manzetti wrote: >> It seems that GMX simply didn't write out the correct frame. The confout.gro >> file written out is written at the same time as the trajectories, and for >> some reason, this confout.gro file has nothing to do with the last output >> frame from the sims, when produced by gmx trjconv.. > confout.gro is the final frame, re-wrapped for PBC. So it may "look" > different from the final frame of the trajectory, but it's not. > > Unless you actually provide answers to the questions I asked and any > actual commands you're issuing (e.g. what did you do when you say > "produced by gmx trjconv" for instance?), then there's nothing anyone > here can do to help you. We can't see what you're seeing or interpret > what's in your mind :) > > -Justin > >> >> >> >> >> Sergio Manzetti >> >> [ http://www.fjordforsk.no/logo_hr2.jpg ] >> >> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | >> ] >> Midtun >> 6894 Vangsnes >> Norge >> Org.nr. 911 659 654 >> Tlf: +47 57695621 >> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | >> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | >> FAP ] >> >> >> >> From: "Justin Lemkul" <jalem...@vt.edu> >> To: "gmx-users" <gmx-us...@gromacs.org> >> Sent: Thursday, September 7, 2017 2:28:23 PM >> Subject: Re: [gmx-users] DPOSRES not working >> >> On 9/7/17 5:28 AM, Sergio Manzetti wrote: >>> Hi Johannes, yes, they are there in both cases: >>> >>> ; Include Position restraint file >>> #ifdef POSRES >>> #include "posre_DNA_chain_E.itp" >>> #endif >>> >> Do you have a position restraint energy term written in your .log file, >> and if so, what is its magnitude? Does your DNA start at the middle of >> the box (GROMACS convention) or at the coordinate origin (like other >> software)? If you watch the trajectory evolve, what happens? Does the >> DNA move a lot or does it just bounce back and forth around its original
Re: [gmx-users] DPOSRES not working
On 9/7/17 8:52 AM, Sergio Manzetti wrote: Hey Justin , you sound like Mark Zuckerberg :) I don't know whether that's good or bad... Here is the command I used: gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 -dump 1 is easier than using -b and -e, FYI. and it gives the write gro with DNA in the box as it should be. So then things worked, yes? This confout.gro is not the same as came out from the GMX run, at the same moment as the TRJ and XTC came In what way? Why does this lead you to believe that your restraints aren't working? The questions I asked before are more diagnostic of whether or not things are functioning. Dumping a (non-PBC-corrected) frame and looking at another one (PBC corrected, albeit perhaps not in the best way) does not say anything about whether or not the algorithms are working. -Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:55:05 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 8:45 AM, Sergio Manzetti wrote: It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. confout.gro is the final frame, re-wrapped for PBC. So it may "look" different from the final frame of the trajectory, but it's not. Unless you actually provide answers to the questions I asked and any actual commands you're issuing (e.g. what did you do when you say "produced by gmx trjconv" for instance?), then there's nothing anyone here can do to help you. We can't see what you're seeing or interpret what's in your mind :) -Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:28:23 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 5:28 AM, Sergio Manzetti wrote: Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Do you have a position restraint energy term written in your .log file, and if so, what is its magnitude? Does your DNA start at the middle of the box (GROMACS convention) or at the coordinate origin (like other software)? If you watch the trajectory evolve, what happens? Does the DNA move a lot or does it just bounce back and forth around its original position (suggesting your box is simply too small and any time an atom crosses a boundary, you get a jump)? -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.
Re: [gmx-users] DPOSRES not working
Hey Justin , you sound like Mark Zuckerberg :) Here is the command I used: gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 and it gives the write gro with DNA in the box as it should be. This confout.gro is not the same as came out from the GMX run, at the same moment as the TRJ and XTC came Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:55:05 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 8:45 AM, Sergio Manzetti wrote: > It seems that GMX simply didn't write out the correct frame. The confout.gro > file written out is written at the same time as the trajectories, and for > some reason, this confout.gro file has nothing to do with the last output > frame from the sims, when produced by gmx trjconv.. confout.gro is the final frame, re-wrapped for PBC. So it may "look" different from the final frame of the trajectory, but it's not. Unless you actually provide answers to the questions I asked and any actual commands you're issuing (e.g. what did you do when you say "produced by gmx trjconv" for instance?), then there's nothing anyone here can do to help you. We can't see what you're seeing or interpret what's in your mind :) -Justin > > > > > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > > > > From: "Justin Lemkul" <jalem...@vt.edu> > To: "gmx-users" <gmx-us...@gromacs.org> > Sent: Thursday, September 7, 2017 2:28:23 PM > Subject: Re: [gmx-users] DPOSRES not working > > On 9/7/17 5:28 AM, Sergio Manzetti wrote: >> Hi Johannes, yes, they are there in both cases: >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre_DNA_chain_E.itp" >> #endif >> > Do you have a position restraint energy term written in your .log file, > and if so, what is its magnitude? Does your DNA start at the middle of > the box (GROMACS convention) or at the coordinate origin (like other > software)? If you watch the trajectory evolve, what happens? Does the > DNA move a lot or does it just bounce back and forth around its original > position (suggesting your box is simply too small and any time an atom > crosses a boundary, you get a jump)? > > -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. -- 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.
Re: [gmx-users] DPOSRES not working
On 9/7/17 8:45 AM, Sergio Manzetti wrote: It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. confout.gro is the final frame, re-wrapped for PBC. So it may "look" different from the final frame of the trajectory, but it's not. Unless you actually provide answers to the questions I asked and any actual commands you're issuing (e.g. what did you do when you say "produced by gmx trjconv" for instance?), then there's nothing anyone here can do to help you. We can't see what you're seeing or interpret what's in your mind :) -Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:28:23 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 5:28 AM, Sergio Manzetti wrote: Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Do you have a position restraint energy term written in your .log file, and if so, what is its magnitude? Does your DNA start at the middle of the box (GROMACS convention) or at the coordinate origin (like other software)? If you watch the trajectory evolve, what happens? Does the DNA move a lot or does it just bounce back and forth around its original position (suggesting your box is simply too small and any time an atom crosses a boundary, you get a jump)? -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.
Re: [gmx-users] DPOSRES not working
It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:28:23 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 5:28 AM, Sergio Manzetti wrote: > Hi Johannes, yes, they are there in both cases: > > ; Include Position restraint file > #ifdef POSRES > #include "posre_DNA_chain_E.itp" > #endif > Do you have a position restraint energy term written in your .log file, and if so, what is its magnitude? Does your DNA start at the middle of the box (GROMACS convention) or at the coordinate origin (like other software)? If you watch the trajectory evolve, what happens? Does the DNA move a lot or does it just bounce back and forth around its original position (suggesting your box is simply too small and any time an atom crosses a boundary, you get a jump)? -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. -- 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.
Re: [gmx-users] DPOSRES not working
On 9/7/17 5:28 AM, Sergio Manzetti wrote: Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Do you have a position restraint energy term written in your .log file, and if so, what is its magnitude? Does your DNA start at the middle of the box (GROMACS convention) or at the coordinate origin (like other software)? If you watch the trajectory evolve, what happens? Does the DNA move a lot or does it just bounce back and forth around its original position (suggesting your box is simply too small and any time an atom crosses a boundary, you get a jump)? -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.
Re: [gmx-users] DPOSRES not working
Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 11:29:03 AM Subject: Re: [gmx-users] DPOSRES not working Okay, but what did you define in your topologies for your DNA chains: #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" Make sure that at the end of these files you have lines stating e.g: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif The same for your other chain. Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp for all the heavy atoms. If you do not have this position restrain file you can generate it with gmx genrestr. Last but not least you can read about position restrains in the manual. All the best Johannes On 07.09.2017 11:15, Sergio Manzetti wrote: > Hi Johannes, it appears so: > > > ; Include forcefield parameters > #include "amber99sb-ildn.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_DNA_chain_E.itp" > #include "topol_DNA_chain_F.itp" > #include "PRB_GMX.itp" > > ; Include water topology > #include "amber99sb-ildn.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "amber99sb-ildn.ff/ions.itp" > > [ system ] > ; Name > CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water > > [ molecules ] > ; Compound #mols > DNA_chain_E 1 > DNA_chain_F 1 > NA 71 > CL 31 > PRB 1 > SOL 16349 > > > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > > > > From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> > To: "gmx-users" <gmx-us...@gromacs.org> > Sent: Thursday, September 7, 2017 11:18:29 AM > Subject: Re: [gmx-users] DPOSRES not working > > Dear Sergio, > > how did you define the position restrain in your topology? Check your > topology and position restrain file. > > All the best > > Johannes > > > On 07.09.2017 11:07, Sergio Manzetti wrote: >> Hello, I am running 5 simulations with the given mdp: >> >> title = DNA in water stabilization >> cpp = /lib/cpp >> include = -I../top >> define = -DPOSRES >> integrator = md >> dt = 0.002 >> nsteps = 1000 >> nstxout = 5000 >> nstvout = 5000 >> nstlog = 5000 >> nstenergy = 300 >> nstxout-compressed = 300 >> compressed-x-grps = PRB SOL NA CL DNA >> energygrps = PRB SOL NA CL DNA >> nstlist = 10 >> ns-type = grid >> rlist = 0.8 >> coulombtype = PME >> rcoulomb = 0.8 >> rvdw = 0.8 >> tcoupl = V-Rescale >> tc-grps = System >> tau-t = 0.1 >> ref-t = 310 >> Pcoupl = No >> tau-p = 1.0 >> compressibility = 4.5e-5 >> ref-p = 1.0 >> gen-vel = yes >> gen-temp = 310 >> gen-seed = 17527 >> constraints = all-bonds >> >> >> and still, the DNA splits into two >> >> Any ideas what could be wrong? >> >> Thanks >> >> Sergio Manzetti >> >> [ http://www.fjordforsk.no/logo_hr2.jpg ] >> >> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | >> ] >> Midtun >> 6894 Vangsnes >> Norge >> Org.nr. 911 659 654 >> Tlf: +47 57695621 >> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | >> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | >> FAP ] >> -- ___
Re: [gmx-users] DPOSRES not working
Okay, but what did you define in your topologies for your DNA chains: #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" Make sure that at the end of these files you have lines stating e.g: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif The same for your other chain. Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp for all the heavy atoms. If you do not have this position restrain file you can generate it with gmx genrestr. Last but not least you can read about position restrains in the manual. All the best Johannes On 07.09.2017 11:15, Sergio Manzetti wrote: Hi Johannes, it appears so: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" #include "PRB_GMX.itp" ; Include water topology #include "amber99sb-ildn.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water [ molecules ] ; Compound #mols DNA_chain_E 1 DNA_chain_F 1 NA 71 CL 31 PRB 1 SOL 16349 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 11:18:29 AM Subject: Re: [gmx-users] DPOSRES not working Dear Sergio, how did you define the position restrain in your topology? Check your topology and position restrain file. All the best Johannes On 07.09.2017 11:07, Sergio Manzetti wrote: Hello, I am running 5 simulations with the given mdp: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = -DPOSRES integrator = md dt = 0.002 nsteps = 1000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300 compressed-x-grps = PRB SOL NA CL DNA energygrps = PRB SOL NA CL DNA nstlist = 10 ns-type = grid rlist = 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = V-Rescale tc-grps = System tau-t = 0.1 ref-t = 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 17527 constraints = all-bonds and still, the DNA splits into two Any ideas what could be wrong? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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.
Re: [gmx-users] DPOSRES not working
Hi Johannes, it appears so: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" #include "PRB_GMX.itp" ; Include water topology #include "amber99sb-ildn.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water [ molecules ] ; Compound #mols DNA_chain_E 1 DNA_chain_F 1 NA 71 CL 31 PRB 1 SOL 16349 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 11:18:29 AM Subject: Re: [gmx-users] DPOSRES not working Dear Sergio, how did you define the position restrain in your topology? Check your topology and position restrain file. All the best Johannes On 07.09.2017 11:07, Sergio Manzetti wrote: > Hello, I am running 5 simulations with the given mdp: > > title = DNA in water stabilization > cpp = /lib/cpp > include = -I../top > define = -DPOSRES > integrator = md > dt = 0.002 > nsteps = 1000 > nstxout = 5000 > nstvout = 5000 > nstlog = 5000 > nstenergy = 300 > nstxout-compressed = 300 > compressed-x-grps = PRB SOL NA CL DNA > energygrps = PRB SOL NA CL DNA > nstlist = 10 > ns-type = grid > rlist = 0.8 > coulombtype = PME > rcoulomb = 0.8 > rvdw = 0.8 > tcoupl = V-Rescale > tc-grps = System > tau-t = 0.1 > ref-t = 310 > Pcoupl = No > tau-p = 1.0 > compressibility = 4.5e-5 > ref-p = 1.0 > gen-vel = yes > gen-temp = 310 > gen-seed = 17527 > constraints = all-bonds > > > and still, the DNA splits into two > > Any ideas what could be wrong? > > Thanks > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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.
Re: [gmx-users] DPOSRES not working
Dear Sergio, how did you define the position restrain in your topology? Check your topology and position restrain file. All the best Johannes On 07.09.2017 11:07, Sergio Manzetti wrote: Hello, I am running 5 simulations with the given mdp: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = -DPOSRES integrator = md dt = 0.002 nsteps = 1000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300 compressed-x-grps = PRB SOL NA CL DNA energygrps = PRB SOL NA CL DNA nstlist = 10 ns-type = grid rlist = 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = V-Rescale tc-grps = System tau-t = 0.1 ref-t = 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 17527 constraints = all-bonds and still, the DNA splits into two Any ideas what could be wrong? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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.
[gmx-users] DPOSRES not working
Hello, I am running 5 simulations with the given mdp: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = -DPOSRES integrator = md dt = 0.002 nsteps = 1000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300 compressed-x-grps = PRB SOL NA CL DNA energygrps = PRB SOL NA CL DNA nstlist = 10 ns-type = grid rlist = 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = V-Rescale tc-grps = System tau-t = 0.1 ref-t = 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 17527 constraints = all-bonds and still, the DNA splits into two Any ideas what could be wrong? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- 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.
