Re: [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)
Hi, PDB format needs atom names but trjcat only knows how to read those from a -s input file. Mark On Thu, 3 Aug 2017 08:34 Andrew Bostick wrote: > Dear gromacs users, > > I have 2 trajectory files as pdb format. > > I want to have only one file using the following command: > > gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime > > I encountered with: > > - > > Command line: > gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime > > Reading frame 0 time0.000'c15 t= 3.0', 6250 atoms > Reading frame 0 time0.000'c15 t= 3.0', 6250 atoms > Reading frame 1 time 3.000 > > > Enter the new start time (ps) for each file. > There are two special options, both disable sorting: > > c (continue) - The start time is taken from the end > of the previous file. Use it when your continuation run > restarts with t=0. > > l (last) - The time in this file will be changed the > same amount as in the previous. Use it when the time in the > new run continues from the end of the previous one, > since this takes possible overlap into account. > > File Current start (ps) New start (ps) > - > 9_ms.pdb0.000 ps 0 >19.pdb0.000 ps 900 > > Summary of files and start times used: > > FileStart time Time step > - > 9_ms.pdb0.000 ps3.000 ps >19.pdb 900.000 ps3.000 ps > > > Back Off! I just backed up mix.pdb to ./#mix.pdb.4# > Reading frame 0 time0.000 > > Continue writing frames from 9_ms.pdb t=0 ps, frame=0 > > --- > Program gmx trjcat, VERSION 5.1.3 > Source code file: > /root/gromacs_source/gromacs-5.1.3/src/gromacs/fileio/trxio.c, line: 557 > > Fatal error: > Can not write a pdb file without atom names > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > --- > > How to resolve this issue? > > Best, > Andrew > -- > 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] Protein coming out of simulation box.
Hello I had performed a 100ns protein simulation with gromacs 5.1.4. After the simulation I observed that the protein is coming out of the box. I have used the following commands to correct it: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb Part of the protein is still out of the box (in the file.pdb). Please suggest. Thank You * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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] Can not write a pdb file without atom names (concatenating 2 pdb files)
Dear Mark, Thanks for your reply. > PDB format needs atom names but trjcat only knows how to read those > from a -s input file. There is no -s option (for tpr file) in the trjcat command. gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime -s md.tpr Error in user input: Invalid command-line options Unknown command-line option -s -- 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] Clustering
Hi all, I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have create a separate tpr file for the molecule of interest. And I had to generate another trajectory file in order for them to match. I run the command below: gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 6 -cut 0.35 -mol I get an error message saying that gromacs only finds 1 cluster but this cannot be right as I can see more than one cluster forming during the simulation Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 Can somebody please advise me on how to overcome this issue? Many thanks, Akash -- 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] Can not write a pdb file without atom names (concatenating 2 pdb files)
Hi, Oh, OK. Well, that's another good reason not to use PDB as a trajectory format. Convert to trr (or produce something better in the first place), concatenate that, and convert to pdb if you have to work with something that requires it. Mark On Thu, 3 Aug 2017 10:31 Andrew Bostick wrote: > Dear Mark, > > Thanks for your reply. > > > PDB format needs atom names but trjcat only knows how to read those > > > from a -s input file. > > > There is no -s option (for tpr file) in the trjcat command. > > gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime -s md.tpr > > Error in user input: > Invalid command-line options > Unknown command-line option -s > -- > 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] Protein coming out of simulation box.
Hi, Please check out the GROMACS FAQs. Your protein can't come out of a periodic cell Mark On Thu, 3 Aug 2017 10:26 wrote: > Hello > > I had performed a 100ns protein simulation with gromacs 5.1.4. > > After the simulation I observed that the protein is coming out of the box. > > I have used the following commands to correct it: > > gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc > > gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb > > Part of the protein is still out of the box (in the file.pdb). > > Please suggest. > > Thank You > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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] evaluation of simulated frames by procheck
Dear gromacs users, I have done simulation of peptide with 28 residues length for 100ns. I have used the OPLS force field. My peptide is disordered peptide and two of its regions have been modeled by using modellar. After modelling I have checked the steriochemical properties of the peptide by procheck and their G-factor value is greater than -0.5. After my simulations I have taken some of the frames randomly and checked the steriochemical properties of them by procheck and I got G-factor value is less than -0.5. If the G-factor value less than the reference value i.e -0.5 the structure has to be validated. I got less G-factor values for my all frames. Now my question comes here. As I didn't get greater G-factor values than reference values, is my simulation not valid? For your information all ramachandran angles are in allowed regions. And also suggest how to defend my simulation is valid. Thanks in advance Surya Graduate student 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.
Re: [gmx-users] Error in itp file
Yes, using ACPYPE is pretty simple. They have a web server, where you can upload your PDB or MOL2 file, provide the charge and multiplicity and it gives you the output file. On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > > > On 8/2/17 12:35 PM, Souvik Dey wrote: > >> Hi, >> >> I just generated an itp file from ACPYPE. However, if I try to add ions it >> shows the following error: >> >> Fatal error: >> Syntax error - File FAD.itp, line 3 >> Last line read: >> '[ atomtypes ]' >> Invalid order for directive atomtypes >> >> >> Can somebody say how do I fix this? >> >> > This exact situation is described here: > > http://www.gromacs.org/Documentation/Errors#Invalid_order_ > for_directive_xxx > > -Justin > > -- > == > > 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 > > == > > -- > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in itp file
Yes, I saw the GROMACS website. But my itp file has [atomtypes] first followed by [moleculetypes]. So, I am still not getting what is the error. On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: > Yes, using ACPYPE is pretty simple. They have a web server, where you can > upload your PDB or MOL2 file, provide the charge and multiplicity and it > gives you the output file. > > On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > >> >> >> On 8/2/17 12:35 PM, Souvik Dey wrote: >> >>> Hi, >>> >>> I just generated an itp file from ACPYPE. However, if I try to add ions >>> it >>> shows the following error: >>> >>> Fatal error: >>> Syntax error - File FAD.itp, line 3 >>> Last line read: >>> '[ atomtypes ]' >>> Invalid order for directive atomtypes >>> >>> >>> Can somebody say how do I fix this? >>> >>> >> This exact situation is described here: >> >> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo >> r_directive_xxx >> >> -Justin >> >> -- >> == >> >> 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 >> >> == >> >> -- >> 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. >> > > > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] mutagenesis- Study the role of an aminoacids in proteins.
Dear all, I wanted to study the role of specific amino acids in a channel protein. Currently working on alanine scanning mutagenesis, by performing two independent simulations of wild and mutant proteins (Also, like to get information regarding structural and functional stability). I would like to know is there any other active method or approaches in MD to provide better and reliable results in this aspects. It will be helpful if anyone can direct me to any articles or pieces of information. Thanks you -- Regards, Nikhil Maroli -- 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] meaning of -sigfac option in gmx sigeps
Hi All, Can anyone help me regarding the -sigfac option in gmx sigeps? What does this -sigfac mean? And, is the C6, C9 terms correspond to the C6, C9 terms in the ffnonbonded.itp? I am using the LJ potential form, U(r) = (27/4)*epsilon [ (sigma/r)^9 - (sigma/r)^6 ] any help would be appreciated -- Tamisra Pal Post Doctoral Research Fellow Technische Universität Darmstadt Institut für Festkörperphysik Hochschulstraße 6 64289 Darmstadt , Germany -- 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] meaning of -sigfac option in gmx sigeps
Hi, gmx help sigeps shows that -sigfac is just sugar for helping inspect the plot. Otherwise, I have no idea. Mark On Thu, Aug 3, 2017 at 4:18 PM Tamisra Pal wrote: > Hi All, > Can anyone help me regarding the -sigfac option in gmx sigeps? > What does this -sigfac mean? > And, is the C6, C9 terms correspond to the C6, C9 terms in the > ffnonbonded.itp? > I am using the LJ potential form, > U(r) = (27/4)*epsilon [ (sigma/r)^9 - (sigma/r)^6 ] > > any help would be appreciated > > > > -- > Tamisra Pal > > Post Doctoral Research Fellow > Technische Universität Darmstadt > Institut für Festkörperphysik > Hochschulstraße 6 > 64289 Darmstadt , Germany > > > > -- > 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] Pulling
Hello, I´m using grimaces 2016 to pull a dihedral angle. With the angle I can force the flipping in and out of a single bulge in a RNA system. I tried with different k. I do a simulation of 180 ns with a rate of 1 degree each ns. I always put the reference at 0 degree I have obtained different results: Sometime when I see the file pullx.xvg it says that my COM is changing but in reality it dose not. When I see the trajectory with VMD I can see that the bulge is not moving. Some other time instead (changing randomly k), the bulge moves, but it dose a rotation of 180 degrees with few steps and for the rest of the simulations stay steady. Some other time it continues 'to be pulled’ and break the structure. Any suggestion? This is the part for the pulling: pull-coord1-geometry = dihedral pull-coord1-groups = 1 2 3 4 5 6 pull-group1-pbcatom= 0 pull_group1_name = phospate_6 pull_group2_name = phospate_8 pull_group3_name = phospate_8 pull_group4_name = U7 pull_group5_name = U7 pull_group6_name = bulge pull_coord1_rate = 1 pull_coord1_k = 100. (I modify this) pull-coord1-start = yes pull-coord1-init = -59.903 Thanks for the help! Luca -- 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] Gromacs 2016 pulling code
Hello, I´m using grimaces 2016 to pull a dihedral angle. With the angle I can force the flipping in and out of a single bulge in a RNA system. I tried with different k. I do a simulation of 180 ns with a rate of 1 degree each ns. I always put the reference at 0 degree I have obtained different results: Sometime when I see the file pullx.xvg it says that my COM is changing but in reality it dose not. When I see the trajectory with VMD I can see that the bulge is not moving. Some other time instead (changing randomly k), the bulge moves, but it dose a rotation of 180 degrees with few steps and for the rest of the simulations stay steady. Some other time it continues 'to be pulled’ and break the structure. Any suggestion? This is the part for the pulling: pull-coord1-geometry = dihedral pull-coord1-groups = 1 2 3 4 5 6 pull-group1-pbcatom= 0 pull_group1_name = phospate_6 pull_group2_name = phospate_8 pull_group3_name = phospate_8 pull_group4_name = U7 pull_group5_name = U7 pull_group6_name = bulge pull_coord1_rate = 1 pull_coord1_k = 100. (I modify this) pull-coord1-start = yes pull-coord1-init = -59.903 Thanks for the help! Luca -- 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] Error in itp file
Can you give web server link? I have tried but didn't find. On Aug 3, 2017 5:53 AM, "Souvik Dey" wrote: > Yes, using ACPYPE is pretty simple. They have a web server, where you can > upload your PDB or MOL2 file, provide the charge and multiplicity and it > gives you the output file. > > On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > > > > > > > On 8/2/17 12:35 PM, Souvik Dey wrote: > > > >> Hi, > >> > >> I just generated an itp file from ACPYPE. However, if I try to add ions > it > >> shows the following error: > >> > >> Fatal error: > >> Syntax error - File FAD.itp, line 3 > >> Last line read: > >> '[ atomtypes ]' > >> Invalid order for directive atomtypes > >> > >> > >> Can somebody say how do I fix this? > >> > >> > > This exact situation is described here: > > > > http://www.gromacs.org/Documentation/Errors#Invalid_order_ > > for_directive_xxx > > > > -Justin > > > > -- > > == > > > > 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 > > > > == > > > > -- > > 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. > > > > > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- > 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] Problems with continuing simulation after time limit
Hi everyone, I am running a simulation of 500 ns using GROMACS 2016 through submitting jobs in our HPC. Due to limited time to run per job, I wrote a bash code to resubmit the job and resume the simulation from a checkpoint. However, I am receiving an error when the following command is run: Command line: gmx_mpi mdrun -s /scratch/sad16109/clavanin/copy/gromacs/part1/part1.tpr -deffnm /scratch/sad16109/clavanin/copy/gromacs/part2/neutral2 -cpi /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt -cpt 100 -cpo /scratch/sad16109/clavanin/copy/gromacs/part2/part2.cpt -maxh 12 the error being issued is: Output file appending has been requested, but some output files listed in the checkpoint file /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt are not present or not named as the output files by the current program: Expect output files present: Expected output files not present or named differently: /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.log /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.trr /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.edr --- Program: gmx mdrun, version 2016 Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177) MPI rank:0 (out of 24) Fatal error: File appending requested, but 3 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 receive that error even if the neutral1.log, neutral1.trr, and neutral1.edr files are present in the "part1" folder. I was using the similar code with Gromacs 5 and I am not having problems. I am not sure if this is something new in Gromacs 2016. I am thinking that there might be something wrong with how I name my files but I am not sure where. Thanks! -- Searle Aichelle S. Duay Ph.D. Student Chemistry Department, University of Connecticut searle.d...@uconn.edu -- 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] Problems with continuing simulation after time limit
Hi, On Thu, Aug 3, 2017 at 8:34 PM Searle Duay wrote: > Hi everyone, > > I am running a simulation of 500 ns using GROMACS 2016 through submitting > jobs in our HPC. Due to limited time to run per job, I wrote a bash code to > resubmit the job and resume the simulation from a checkpoint. It is much easier to just do mpirun gmx_mpi mdrun -cpi for the default appending behaviour, or mpirun gmx_mpi mdrun -cpi -noappend for getting each part written to a different numbered set of output files. The latter gives you the job of pasting things together later on. However, I > am receiving an error when the following command is run: > > Command line: > gmx_mpi mdrun -s /scratch/sad16109/clavanin/copy/gromacs/part1/part1.tpr > -deffnm /scratch/sad16109/clavanin/copy/gromacs/part2/neutral2 -cpi > /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt -cpt 100 -cpo > /scratch/sad16109/clavanin/copy/gromacs/part2/part2.cpt -maxh 12 > As it says, the file you passed to -cpi was written when the output files had different names, yet you've asked mdrun to default to appending to the old output files. mdrun doesn't know which error you've made. > the error being issued is: > > Output file appending has been requested, > but some output files listed in the checkpoint file > /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt > are not present or not named as the output files by the current program: > Expect output files present: > > Expected output files not present or named differently: > /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.log > /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.trr > /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.edr > > --- > Program: gmx mdrun, version 2016 > Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177) > MPI rank:0 (out of 24) > > Fatal error: > File appending requested, but 3 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 receive that error even if the neutral1.log, neutral1.trr, and > neutral1.edr files are present in the "part1" folder. I was using the > similar code with Gromacs 5 and I am not having problems. I am not sure if > this is something new in Gromacs 2016. > It's new, exactly as the message says it is, because the old behaviour made it easy for people to over-write their trajectory files within meaning to. > I am thinking that there might be something wrong with how I name my files > but I am not sure where. > Very likely you're just doing more work than you need to be / should be doing. Mark > Thanks! > > -- > Searle Aichelle S. Duay > Ph.D. Student > Chemistry Department, University of Connecticut > searle.d...@uconn.edu > -- > 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] Error in itp file
write the ligand topology just after the forcefield parameter. ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include ligand topology #include "drg.itp" On Thu, Aug 3, 2017 at 5:53 AM, Souvik Dey wrote: > Yes, I saw the GROMACS website. But my itp file has [atomtypes] first > followed by [moleculetypes]. So, I am still not getting what is the error. > > On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: > > > Yes, using ACPYPE is pretty simple. They have a web server, where you can > > upload your PDB or MOL2 file, provide the charge and multiplicity and it > > gives you the output file. > > > > On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > > > >> > >> > >> On 8/2/17 12:35 PM, Souvik Dey wrote: > >> > >>> Hi, > >>> > >>> I just generated an itp file from ACPYPE. However, if I try to add ions > >>> it > >>> shows the following error: > >>> > >>> Fatal error: > >>> Syntax error - File FAD.itp, line 3 > >>> Last line read: > >>> '[ atomtypes ]' > >>> Invalid order for directive atomtypes > >>> > >>> > >>> Can somebody say how do I fix this? > >>> > >>> > >> This exact situation is described here: > >> > >> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo > >> r_directive_xxx > >> > >> -Justin > >> > >> -- > >> == > >> > >> 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 > >> > >> == > >> > >> -- > >> 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. > >> > > > > > > > > -- > > Souvik Dey > > Integrated Science Education & Research Centre > > Visva Bharati University > > Santiniketan-731235 > > West Bengal > > 8981736643 > > > > > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- > 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. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] segmentation fault for unknown reason
On 8/2/17 3:23 PM, gangotri dey wrote: Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following minim.mdp there is segmentation error as follows. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 50; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Error: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= 3.46301e+34 Fmax= 2.91045e+06, atom= 289 [fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal 11) ./script: line 5: 54036 Segmentation fault (core dumped) gmx_mpi mdrun -ntomp 1 -v -deffnm em I do not understand this problem. Is there anything wrong with my structure or the minim.mdp? It's either the coordinates or the force field parameters. You have a configuration with an energy on the order of 10^34 kJ/mol, which is essentially infinite, so something is fundamentally flawed. -Justin -- == 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 == -- 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] Error in itp file
On 8/3/17 8:53 AM, Souvik Dey wrote: Yes, I saw the GROMACS website. But my itp file has [atomtypes] first followed by [moleculetypes]. So, I am still not getting what is the error. All [atomtypes] (and more generally, any force field parameters) must appear before *any* [moleculetype] directives, not just the one to which the parameters apply. So a topology that introduces parameters must be #included before any invocation of a [moleculetype]. -Justin On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: Yes, using ACPYPE is pretty simple. They have a web server, where you can upload your PDB or MOL2 file, provide the charge and multiplicity and it gives you the output file. On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: On 8/2/17 12:35 PM, Souvik Dey wrote: Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I fix this? This exact situation is described here: http://www.gromacs.org/Documentation/Errors#Invalid_order_fo r_directive_xxx -Justin -- == 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 == -- 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. -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- == 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 == -- 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.
