Re: [gmx-users] simulation continuation without -t option
Thanks a lot Mark! Prabir On Thu, Sep 19, 2019 at 9:50 PM Mark Abraham wrote: > Hi, > > As you can see in gmx help grompp, you should use -t when you want a high > fidelity restart. Obviously, then you would not also choose to generate > velocities (though I forget what takes priority over the velocities in that > case) > > Mark > > On Fri., 20 Sep. 2019, 01:05 Prabir Khatua, > wrote: > > > Thank you very much Mark! > > > > I could see that the velocities exactly match with what was there in the > > initial .gro file that was used with -f option. > > This means that -t option is optional in this case provided one uses > > gen_vel as no. I am still confused when one > > should use -t option. Is it like -t option ensures to use the last > position > > and coordinates even though one mentions > > gen_vel as yes in .mdp file? > > > > Sincerely, > > > > Prabir > > > > On Thu, Sep 19, 2019 at 12:08 PM Mark Abraham > > wrote: > > > > > Hi, > > > > > > If grompp sees that your .mdp file asks for it to generate velocities, > it > > > does so and reports it in the terminal output. You will see that for > your > > > NVT grompp and not for your NPT grompp. > > > > > > You can also use gmx dump -s the.tpr to observe whether the velocities > > > match the input you gave to the NPT grompp. > > > > > > Mark > > > > > > On Thu, 19 Sep 2019 at 18:58, Prabir Khatua > > > wrote: > > > > > > > Hello Gromacs users, > > > > > > > > I have a confusion about generating tpr file from .gro. I have not > used > > > -t > > > > option while > > > > generating .tpr file. Please note that in this case, I first did a > > > > simulation in NVT ensemble > > > > followed by NPT ensemble. In case of NPT run, I am using gen_vel > option > > > as > > > > no in the mdp file and the last gro file that I used for generating > tpr > > > for > > > > the next run (NVT) had both position and velocities. However, the > > output > > > of > > > > grompp option showed a seed value but I am not sure whether it was > same > > > as > > > > that of the NVT run. So my concern is whether it considered the > > > velocities > > > > from the .gro file or it generated a new set of velocities. If it > > > > generated the new set of velocities, can anyone tell me what was the > > job > > > of > > > > -c option corresponding to .gro file that contained both position and > > > > velocities or -c option works for only position? Any help would be > > > > appreciated. > > > > > > > > Thanks in advance! > > > > > > > > Prabir > > > > > > > > -- > > > > > > > > *Prabir Khatua* > > > > *Postdoctoral Research Associate* > > > > *Department of Chemistry & Biochemistry* > > > > *University of Oklahoma* > > > > *Norman, Oklahoma 73019* > > > > *U. S. A.* > > > > -- > > > > 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. > > > > > > > > > -- > > > > *Prabir Khatua* > > *Postdoctoral Research Associate* > > *Department of Chemistry & Biochemistry* > > *University of Oklahoma* > > *Norman, Oklahoma 73019* > > *U. S. A.* > > -- > > 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. > -- *Prabir Khatua* *Postdoctoral Research Associate* *Department of Chemistry & Biochemistry* *University of Oklahoma* *Norman, Oklahoma 73019* *U. S. A.* -- 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
Re: [gmx-users] simulation continuation without -t option
Hi, As you can see in gmx help grompp, you should use -t when you want a high fidelity restart. Obviously, then you would not also choose to generate velocities (though I forget what takes priority over the velocities in that case) Mark On Fri., 20 Sep. 2019, 01:05 Prabir Khatua, wrote: > Thank you very much Mark! > > I could see that the velocities exactly match with what was there in the > initial .gro file that was used with -f option. > This means that -t option is optional in this case provided one uses > gen_vel as no. I am still confused when one > should use -t option. Is it like -t option ensures to use the last position > and coordinates even though one mentions > gen_vel as yes in .mdp file? > > Sincerely, > > Prabir > > On Thu, Sep 19, 2019 at 12:08 PM Mark Abraham > wrote: > > > Hi, > > > > If grompp sees that your .mdp file asks for it to generate velocities, it > > does so and reports it in the terminal output. You will see that for your > > NVT grompp and not for your NPT grompp. > > > > You can also use gmx dump -s the.tpr to observe whether the velocities > > match the input you gave to the NPT grompp. > > > > Mark > > > > On Thu, 19 Sep 2019 at 18:58, Prabir Khatua > > wrote: > > > > > Hello Gromacs users, > > > > > > I have a confusion about generating tpr file from .gro. I have not used > > -t > > > option while > > > generating .tpr file. Please note that in this case, I first did a > > > simulation in NVT ensemble > > > followed by NPT ensemble. In case of NPT run, I am using gen_vel option > > as > > > no in the mdp file and the last gro file that I used for generating tpr > > for > > > the next run (NVT) had both position and velocities. However, the > output > > of > > > grompp option showed a seed value but I am not sure whether it was same > > as > > > that of the NVT run. So my concern is whether it considered the > > velocities > > > from the .gro file or it generated a new set of velocities. If it > > > generated the new set of velocities, can anyone tell me what was the > job > > of > > > -c option corresponding to .gro file that contained both position and > > > velocities or -c option works for only position? Any help would be > > > appreciated. > > > > > > Thanks in advance! > > > > > > Prabir > > > > > > -- > > > > > > *Prabir Khatua* > > > *Postdoctoral Research Associate* > > > *Department of Chemistry & Biochemistry* > > > *University of Oklahoma* > > > *Norman, Oklahoma 73019* > > > *U. S. A.* > > > -- > > > 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. > > > > > -- > > *Prabir Khatua* > *Postdoctoral Research Associate* > *Department of Chemistry & Biochemistry* > *University of Oklahoma* > *Norman, Oklahoma 73019* > *U. S. A.* > -- > 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.
[gmx-users] Functional dynamics in gromacs
Dear Users, I am working in a project, and I need to perform functional dynamics. I would like to associate local movements in the active sites with important function of a set of proteins. I wonder if someone have used it before, and if so, I would bet you to share a tutorial to do it. I used to run molecular dynamics in gromacs parallel. Thanks in advance for your support. Kind regards. -- 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] simulation continuation without -t option
Thank you very much Mark! I could see that the velocities exactly match with what was there in the initial .gro file that was used with -f option. This means that -t option is optional in this case provided one uses gen_vel as no. I am still confused when one should use -t option. Is it like -t option ensures to use the last position and coordinates even though one mentions gen_vel as yes in .mdp file? Sincerely, Prabir On Thu, Sep 19, 2019 at 12:08 PM Mark Abraham wrote: > Hi, > > If grompp sees that your .mdp file asks for it to generate velocities, it > does so and reports it in the terminal output. You will see that for your > NVT grompp and not for your NPT grompp. > > You can also use gmx dump -s the.tpr to observe whether the velocities > match the input you gave to the NPT grompp. > > Mark > > On Thu, 19 Sep 2019 at 18:58, Prabir Khatua > wrote: > > > Hello Gromacs users, > > > > I have a confusion about generating tpr file from .gro. I have not used > -t > > option while > > generating .tpr file. Please note that in this case, I first did a > > simulation in NVT ensemble > > followed by NPT ensemble. In case of NPT run, I am using gen_vel option > as > > no in the mdp file and the last gro file that I used for generating tpr > for > > the next run (NVT) had both position and velocities. However, the output > of > > grompp option showed a seed value but I am not sure whether it was same > as > > that of the NVT run. So my concern is whether it considered the > velocities > > from the .gro file or it generated a new set of velocities. If it > > generated the new set of velocities, can anyone tell me what was the job > of > > -c option corresponding to .gro file that contained both position and > > velocities or -c option works for only position? Any help would be > > appreciated. > > > > Thanks in advance! > > > > Prabir > > > > -- > > > > *Prabir Khatua* > > *Postdoctoral Research Associate* > > *Department of Chemistry & Biochemistry* > > *University of Oklahoma* > > *Norman, Oklahoma 73019* > > *U. S. A.* > > -- > > 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. > -- *Prabir Khatua* *Postdoctoral Research Associate* *Department of Chemistry & Biochemistry* *University of Oklahoma* *Norman, Oklahoma 73019* *U. S. A.* -- 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] Simulated Annealing Procedure
Hello gromacs users, My goal is to do a better conformational sampling of my peptides in vacuum. I was wondering do I simulated annealing with position restraints or not? Many thanks, Neena -- 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] Tesla GPUs: P40 or P100?
Hi, I strongly recommend the Quadro RTX series, 6000 or 5000. These should not be a lot more expensive, but will be a lot faster than the Pascal generation cards. For comparisons see our recent paper: https://doi.org/10.1002/jcc.26011 Cheers, -- Szilárd On Thu, Sep 19, 2019, 09:50 Matteo Tiberti wrote: > Hi all, > > we are considering getting a new server, mainly for GROMACS and for other > CPU-intensive tasks. > > Unfortunately we are unable to buy consumer GPUs and we need to get Teslas > to accelerate GROMACS and possibly for other MD workload in the future. > Both P40 and P100 fit our budget, and I'd be inclined towards the P40 for > the slightly better single-precision performance and larger memory. The P40 > has however lower bandwidth and much lower double-precision performance > respect > to the P100 (it's more similar to a consumer GPU in this extent), which > shouldn't matter as far as GROMACS is concerned right now. I've seen some > talk in the mailing list about implementing mixed/fixed precision modes in > GROMACS, and for what I gathered it's unlikely to happen anytime soon, so I > believe the P40 to be a future-proof choice (at least in the short-medium > term). > > This said, I feel like the P40 isn't getting much recognition both in the > mailing list and in the "bang for your bucks" papers - so my question boils > down to, is there any reason we should prefer the P100 card over the P40? > > Thanks for your help! > > Matteo > -- > 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.
[gmx-users] CHARMM GUI membrane builder's assembled output
Greetings, I used charmm gui's custom Membrane/protein builder to assemble components for MD simulation. It gave me equillibriated box. I am confused whether I should equllibriate box again or not? From which step should I start in Gromac,Energy minimization, equillibriation or Production MD? -- 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] simulation continuation without -t option
Hi, If grompp sees that your .mdp file asks for it to generate velocities, it does so and reports it in the terminal output. You will see that for your NVT grompp and not for your NPT grompp. You can also use gmx dump -s the.tpr to observe whether the velocities match the input you gave to the NPT grompp. Mark On Thu, 19 Sep 2019 at 18:58, Prabir Khatua wrote: > Hello Gromacs users, > > I have a confusion about generating tpr file from .gro. I have not used -t > option while > generating .tpr file. Please note that in this case, I first did a > simulation in NVT ensemble > followed by NPT ensemble. In case of NPT run, I am using gen_vel option as > no in the mdp file and the last gro file that I used for generating tpr for > the next run (NVT) had both position and velocities. However, the output of > grompp option showed a seed value but I am not sure whether it was same as > that of the NVT run. So my concern is whether it considered the velocities > from the .gro file or it generated a new set of velocities. If it > generated the new set of velocities, can anyone tell me what was the job of > -c option corresponding to .gro file that contained both position and > velocities or -c option works for only position? Any help would be > appreciated. > > Thanks in advance! > > Prabir > > -- > > *Prabir Khatua* > *Postdoctoral Research Associate* > *Department of Chemistry & Biochemistry* > *University of Oklahoma* > *Norman, Oklahoma 73019* > *U. S. A.* > -- > 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.
[gmx-users] simulation continuation without -t option
Hello Gromacs users, I have a confusion about generating tpr file from .gro. I have not used -t option while generating .tpr file. Please note that in this case, I first did a simulation in NVT ensemble followed by NPT ensemble. In case of NPT run, I am using gen_vel option as no in the mdp file and the last gro file that I used for generating tpr for the next run (NVT) had both position and velocities. However, the output of grompp option showed a seed value but I am not sure whether it was same as that of the NVT run. So my concern is whether it considered the velocities from the .gro file or it generated a new set of velocities. If it generated the new set of velocities, can anyone tell me what was the job of -c option corresponding to .gro file that contained both position and velocities or -c option works for only position? Any help would be appreciated. Thanks in advance! Prabir -- *Prabir Khatua* *Postdoctoral Research Associate* *Department of Chemistry & Biochemistry* *University of Oklahoma* *Norman, Oklahoma 73019* *U. S. A.* -- 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] Amber 14SB force-field problem with residue HID
Dear Kenvin, I am Viet Man, who converted amber14sb to gromacs version. The below link is my test to compare energy difference of several amber force fields, gromacs official ones (ff99 and ff99sb) and my converted ones (amber12sb and ammber14sb). The result showed that my converted force fields as good as the the GROMACS official ones in term of energy comparison. http://www.gromacs.org/@api/deki/files/254/=ffA2G_test.pdf I have not carefully looked at other residues except twenty standard residues reported in the test. Your problem is similar as the one of HIP residue, which was posted in GROMACS forum and I have fixed it. You may do search HIP amber14SB and following the solution to fix the issue of HID. Otherwise, I will fix this HID issue by this weekend. Yours sincerely, Viet Man 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. gmx trjorder help (Pandya, Akash) >2. Re: Amber 14SB force-field problem with residue HID (Kevin) >3. -t option? (Hadi Rahmaninejad) >4. Re: -t option? (Mahdi Bagherpoor) >5. Tetrahedral Order Parameter (m g) >6. Re: Tetrahedral Order Parameter (Dallas Warren) > > > -- > > Message: 1 > Date: Wed, 18 Sep 2019 12:59:26 + > From: "Pandya, Akash" > To: "gmx-us...@gromacs.org" > Subject: [gmx-users] gmx trjorder help > Message-ID: > > > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > I used gmx trjorder to order my ligand molecules based on the distance > from the COM of my protein using the command below: > > gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -o ordered.gro > -nshell nshell1.xvg -b 2 -e 2 -na 10 -r 0.5 > > > > I viewed the nshell1.xvg file to see how many ligand molecules were found > within the shell at a particular time. I know in the gromacs manual it > says "When an index group of the first n waters is made, the ordered > trajectory can be used with any GROMACS program to analyze the n closest > waters". I presume that I can use this for my ligand molecules too. > > The problem I have with this is the "ordered" trajectory file contains all > the ligand molecules even the ones not within the cut-off. Can anybody > help with this? > > > Akash > > > > -- > > Message: 2 > Date: Wed, 18 Sep 2019 10:14:13 -0400 > From: Kevin > To: Gromacs Users List > Subject: Re: [gmx-users] Amber 14SB force-field problem with residue > HID > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Thank you Justin for your reply. I totally understand the risk of using a > user-contributed force-field. And that is why I am trying to fix it (and > test it). Then I rather put my question more as a force-field building > question, asking how pdb2gmx generates the list of impropers from the > topology. Hope you could share your experience on this so I could fix it > by > myself. > > Thanks, > Kevin > > On Thu, 12 Sep 2019 at 19:08, Kevin wrote: > >> Dear Users, >> >> I have encountered a problem with the Amber force-field downloaded from >> http://www.gromacs.org/Downloads/User_contributions/Force_fields. >> Whenever I feed this forcefield to pdb2gmx and get a residue HID for >> protein topology, it will cause error message: "No default Proper Dih. >> types". This error can simply be solved by swapping the second and third >> indices on the line number given with the error message. >> >> I tried to dig into the reason behind this error. First, the error line >> contains atomtypes in a sequence of "CT CC CV NA" which CANNOT be >> found >> in ffbonded.itp. Instead, "CT CV CC NA" can be found in ffbonded.itp >> and >> I guess that is why my solution worked. However, when I look at the >> topology of HID, I was confused: >> >> [ impropers ] >> -CCA N H >> CA+N C O >> CG CE1 ND1 HD1 >> CG NE2 CD2 HD2 >>ND1 NE2 CE1 HE1 >>ND1 CD2CGCB >> >> Converting from atom name to atomtypes, there is no either "CT CC CV >> NA" or "CT CV CC NA" in impropers. However, "ND1 CD2CGCB" >> is >> very likely to be the folk just written in a reversed sequence. More >> interestingly, I gave a try on the Amber ff99*-ILDN forcefield, the HID >> topology appears to be nearly the same but no error message was >>
Re: [gmx-users] -t option?
Thank you Peter, Best, Hadi On Thu, Sep 19, 2019 at 8:29 AM Peter Kroon wrote: > Hi Hadi, > > > to expand a little on Mahdi's (correct) answer: > > The checkpoint file contains coordinates and velocities in full > precision (unlike .gro and .xtc files). In addition, it contains the > state of the thermostat and barostat (if applicable). The > thermo/barostat states are not present in the gro/mdp/tpr files, since > they depend on the history of your system. Because of this, including > the checkpoint file to continue your simulation is always a good idea. > > See also: `gmx mdrun -h` and `gmx grompp -h`. > > > Peter > > On 19-09-19 05:13, Hadi Rahmaninejad wrote: > > Thanks Mehdi, > > > > Best, > > Hadi > > > > On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor > > > wrote: > > > >> Hi Hadi, > >> > >> It is well explained in Gromacs tutorial, in the below: > >> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html > >> > >> "Note that we are now including the -t flag to include the checkpoint > file > >> from the *NVT* equilibration" > >> > >> Cheers, > >> Mahdi > >> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad < > ha.rahma...@gmail.com> > >> wrote: > >> > >>> Hello dear users, > >>> > >>> I am going to run a simulation according to a tutorial, but there is an > >>> option of "-t nvt.cpt" that I don't know what is it, and I couldn't > find > >>> any explanation for that. I appreciate if any of you can give me a > short > >>> description of what is that doing, > >>> > >>> Best wishes, > >>> Hadi > >>> -- > >>> 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. > >> > > -- > 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] -t option?
Hi Hadi, to expand a little on Mahdi's (correct) answer: The checkpoint file contains coordinates and velocities in full precision (unlike .gro and .xtc files). In addition, it contains the state of the thermostat and barostat (if applicable). The thermo/barostat states are not present in the gro/mdp/tpr files, since they depend on the history of your system. Because of this, including the checkpoint file to continue your simulation is always a good idea. See also: `gmx mdrun -h` and `gmx grompp -h`. Peter On 19-09-19 05:13, Hadi Rahmaninejad wrote: > Thanks Mehdi, > > Best, > Hadi > > On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor > wrote: > >> Hi Hadi, >> >> It is well explained in Gromacs tutorial, in the below: >> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html >> >> "Note that we are now including the -t flag to include the checkpoint file >> from the *NVT* equilibration" >> >> Cheers, >> Mahdi >> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad >> wrote: >> >>> Hello dear users, >>> >>> I am going to run a simulation according to a tutorial, but there is an >>> option of "-t nvt.cpt" that I don't know what is it, and I couldn't find >>> any explanation for that. I appreciate if any of you can give me a short >>> description of what is that doing, >>> >>> Best wishes, >>> Hadi >>> -- >>> 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. >> -- 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] Center of mass of ligand
Dear all, I want to calculate the centre of the mass of ligand. I have performed the umbrella sampling and pulled the ligand in a specific vector. Now I want to check the ligand centre of mass in the vector. As I know it is possible if I consider two groups but not for single-molecule. Still, I can use gmx traj but it is giving me coordinates of the centre of mass but that is not what I wanted. Any help would be appreciated. Thanks and Regards, Naveen BK, MSc in bioinformatics, +918123474717. -- 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] Energy minimization problem for POPE/POPG soluted bilayer taken from M. Karttunen website
Dear users I tried energy minimization of POPE/POPG bilayer from http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces have not converged to requested precision (output shown below). I used Gromacs version 2019.2 . My colleague also used this bilayer before with earlier version of Gromacs (don't know which one, sorry, few years ago), and everything works fine. I tried a few different bilayers constructed from this one, and noticed that different atoms causes a problem (Fmax on it) but each time it's about H6 atom in some DPO molecule. I checked, and there is no steric clashes with periodic images or solution molecules. Any suggestions what could be wrong? Thanks Below are tipical gromacs output and mdp file: * Gromacs output: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= -3.45240e+05 Fmax= 6.29238e+03, atom= 5580 Step=1, Dmax= 1.0e-02 nm, Epot= -3.51348e+05 Fmax= 3.62527e+03, atom= 1772 Step=2, Dmax= 1.2e-02 nm, Epot= -3.55043e+05 Fmax= 1.07906e+04, atom= 1772 Step=3, Dmax= 1.4e-02 nm, Epot= -3.58399e+05 Fmax= 6.04668e+03, atom= 524 Step=4, Dmax= 1.7e-02 nm, Epot= -3.58764e+05 Fmax= 1.66084e+04, atom= 524 Step=5, Dmax= 2.1e-02 nm, Epot= -3.62991e+05 Fmax= 3.55133e+04, atom= 6325 Step=6, Dmax= 2.5e-02 nm, Epot= -3.66326e+05 Fmax= 3.14946e+05, atom= 6325 Step=7, Dmax= 3.0e-02 nm, Epot= -3.66358e+05 Fmax= 6.27472e+04, atom= 6005 Step=8, Dmax= 3.6e-02 nm, Epot= -3.70907e+05 Fmax= 7.76457e+05, atom= 6217 Step= 10, Dmax= 2.1e-02 nm, Epot= -3.71321e+05 Fmax= 1.24828e+06, atom= 5581 Step= 14, Dmax= 3.2e-03 nm, Epot= -4.38973e+05 Fmax= 7.26301e+07, atom= 5583 Step= 18, Dmax= 4.8e-04 nm, Epot= -4.39005e+05 Fmax= 1.17286e+08, atom= 5581 Step= 28, Dmax= 1.1e-06 nm, Epot= -4.39005e+05 Fmax= 1.16818e+08, atom= 5581 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. *** minim.mdp: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc= xyz * -- 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] Tesla GPUs: P40 or P100?
Hi all, we are considering getting a new server, mainly for GROMACS and for other CPU-intensive tasks. Unfortunately we are unable to buy consumer GPUs and we need to get Teslas to accelerate GROMACS and possibly for other MD workload in the future. Both P40 and P100 fit our budget, and I'd be inclined towards the P40 for the slightly better single-precision performance and larger memory. The P40 has however lower bandwidth and much lower double-precision performance respect to the P100 (it's more similar to a consumer GPU in this extent), which shouldn't matter as far as GROMACS is concerned right now. I've seen some talk in the mailing list about implementing mixed/fixed precision modes in GROMACS, and for what I gathered it's unlikely to happen anytime soon, so I believe the P40 to be a future-proof choice (at least in the short-medium term). This said, I feel like the P40 isn't getting much recognition both in the mailing list and in the "bang for your bucks" papers - so my question boils down to, is there any reason we should prefer the P100 card over the P40? Thanks for your help! Matteo -- 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.
