Re: [gmx-users] Convert-tpr pbc problem for membrane protein
Gromacs shrink the box in x and y direction and prolong in z direction when recording the trajectory. And when loading the trr files directly I can see the lipid is wrapped. Based on some analysis of the protein I think the simulation is fine and it should be just a visualization problem. My system is not symmetric in z direction, with the position of the lipid higher than the initial box center. Do you have any idea how to fix it? Or usually how would you deal with the trajectory of charmm-gui? On 4/16/15 3:11 PM, wh wrote: > Dear Gromacs users, > > > > I recently used Charmm-gui Gromacs input generator to build some input > files for a membrane protein system and ran several simulation with them. > Recommended by charmm-gui README file I used convert-tpr to perform > continuous simulation. Thus the trajectory itself will have some crazy > behavior, with protein in parts and lipid deformed. I managed to > restore the I don't see how using convert-tpr (which is the normal way to extend a run) will inherently lead to "crazy behavior." > protein and generate a trajectory with just protein. However, now I > have a problem to transform the whole system including lipid and > water, ions. No matter what I tried the lipid will still have a > bizarre shape. Does anyone have experience with this issue? Any suggestion will be greatly appreciated. You'll have to provide some actual commands of what you're doing to deal with periodicity and likely upload some images of what you're defining as "bizarre shape." If the molecules were actually distorted, the simulation would have crashed. Likely whatever you're doing with trjconv is wrong. Note that the CHARMM convention is to center the system at the coordinate origin, whereas in GROMACS the center is (x/2, y/2, z/2). So you have to generate a properly centered reference state before doing anything else. There will be several steps to the process, but it is perfectly possible to re-image a trajectory run with a CHARMM-GUI starting structure; we do it routinely. -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.
[gmx-users] Convert-tpr pbc problem for membrane protein
Dear Gromacs users, I recently used Charmm-gui Gromacs input generator to build some input files for a membrane protein system and ran several simulation with them. Recommended by charmm-gui README file I used convert-tpr to perform continuous simulation. Thus the trajectory itself will have some crazy behavior, with protein in parts and lipid deformed. I managed to restore the protein and generate a trajectory with just protein. However, now I have a problem to transform the whole system including lipid and water, ions. No matter what I tried the lipid will still have a bizarre shape. Does anyone have experience with this issue? Any suggestion will be greatly appreciated. Thanks! Han -- 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] gromacs.org_gmx-users Digest, Vol 128, Issue 12
Message: 4 Date: Wed, 03 Dec 2014 16:49:28 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 11 Message-ID: <547f8568.7040...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 12/3/14 4:46 PM, wh wrote: > > > > > > > > > Hi, > > OK, that may be a bug, but I can't imagine why only you experience it. > Please file an issue at http://redmine.gromacs.org and attach (at > least) the files you're using for the restart and the commands with > which you used them. > > Mark > > On Wed, Dec 3, 2014 at 7:55 PM, wh wrote: > >> >> >>>>> Dear Gromacs Users, >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> Recently when I tried to restart a md simulation from previous one >>> >>>>> using convert-tpr with version 5.0.1 , the task failed giving the >>>>> error >>> message: >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> X particles communicated to PME node Y are more than a cell length >>>>> out >>> >>>>> of the domain decomposition cell of their charge group >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> I tried several way to solve it, including modify the >>>>> equilibration >>> >>>>> setting as it said in the gromacs error page, and all failed. If I >>> >>>>> just run one simulation for a long time, it will not crash, at >>>>> least >>> >>>>> can do further than the time point it crashed when using restart. >>> >>>>> >>> >>>>> Does anyone have any idea why this happen and how to solve it? I >>>>> used >>> >>>>> the >>> >>>>> syntax: >>> >>>>> >>> >>>>> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o >>>>> output.tpr >>> >>>>> -extend >>> >>>>> 1 >>> >>>>> >>> >>>>> Any suggestion will be greatly appreciated >>> >>>>> >>> >>> >>> >>>> Do not supply .trr and .edr files; just increase the number of >>>> steps and >>> continue from the existing checkpoint with mdrun -cpi. What you're >>> doing is based on ancient syntax that is no longer relevant. I'm >>> guessing that you're probably winding up with discontinuous states >>> somehow. >>> >>> >>> >>>> >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#V >>> er >>> sion_ >>> 4_and_Newer >>> >>> >>> >>>> -Justin >>> >>> >>> >>> Thank you so much for your timely reply, yet I tried mdrun -s >>> input.tpr -cpi input.cpt -append >>> >>> It still gave the same error message. Could it be a bug? Or I did >>> something wrong? >> >> >> Bug is possible but unlikely. We definitely don't have enough >> information to tell because we've gotten half of it each time - what >> was the conversion >> + restart combination you actually used? Does the original run stay >> + stable >> if it is not interrupted? >> >> Mark >> >> >> >> >> >> >> If I run a long time simulation continuously it can stay stable. I >> just want to run it in smaller jobs or restart it from a check point >> because of the limit on computing resources. Suggested by Justin I >> used syntax: >> mdrun -s input.tpr -cpi input.cpt -append, using the cpt file from >> the previous simulation yet it still gave the same error 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. >> > > > > The thing is I am trying to use the new charm-gui gromacs input > generator, maybe that's the problem. > If there's an issue there, your simulation should crash immediately, not upon continuation from a previous point. -Justin As I checked the trajectory file before, there is an "protein out of box" issue. I modified the pbc to fix it. I am not very familiar with the mechanism here yet I am wondering is it possible when restart from previous file, gromacs failed to modify the pbc and thus resulted in this problem? -- 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] gromacs.org_gmx-users Digest, Vol 128, Issue 11
Hi, OK, that may be a bug, but I can't imagine why only you experience it. Please file an issue at http://redmine.gromacs.org and attach (at least) the files you're using for the restart and the commands with which you used them. Mark On Wed, Dec 3, 2014 at 7:55 PM, wh wrote: > > > > >> Dear Gromacs Users, > > > > >> > > > > >> > > > > >> > > > > >> Recently when I tried to restart a md simulation from previous > > >> one > > > > >> using convert-tpr with version 5.0.1 , the task failed giving the > > >> error > > message: > > > > >> > > > > >> > > > > >> > > > > >> X particles communicated to PME node Y are more than a cell > > >> length out > > > > >> of the domain decomposition cell of their charge group > > > > >> > > > > >> > > > > >> > > > > >> I tried several way to solve it, including modify the > > >> equilibration > > > > >> setting as it said in the gromacs error page, and all failed. If > > >> I > > > > >> just run one simulation for a long time, it will not crash, at > > >> least > > > > >> can do further than the time point it crashed when using restart. > > > > >> > > > > >> Does anyone have any idea why this happen and how to solve it? I > > >> used > > > > >> the > > > > >> syntax: > > > > >> > > > > >> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o > > >> output.tpr > > > > >> -extend > > > > >> 1 > > > > >> > > > > >> Any suggestion will be greatly appreciated > > > > >> > > > > > > > > >Do not supply .trr and .edr files; just increase the number of > > >steps and > > continue from the existing checkpoint with mdrun -cpi. What you're > > doing is based on ancient syntax that is no longer relevant. I'm > > guessing that you're probably winding up with discontinuous states > > somehow. > > > > > > > > > > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#V > > er > > sion_ > > 4_and_Newer > > > > > > > > >-Justin > > > > > > > > Thank you so much for your timely reply, yet I tried mdrun -s > > input.tpr -cpi input.cpt -append > > > > It still gave the same error message. Could it be a bug? Or I did > > something wrong? > > > Bug is possible but unlikely. We definitely don't have enough > information to tell because we've gotten half of it each time - what > was the conversion > + restart combination you actually used? Does the original run stay > + stable > if it is not interrupted? > > Mark > > > > > > > If I run a long time simulation continuously it can stay stable. I > just want to run it in smaller jobs or restart it from a check point > because of the limit on computing resources. Suggested by Justin I > used syntax: > mdrun -s input.tpr -cpi input.cpt -append, using the cpt file from the > previous simulation yet it still gave the same error 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. > The thing is I am trying to use the new charm-gui gromacs input generator, maybe that's the problem. -- 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] gromacs.org_gmx-users Digest, Vol 128, Issue 10
> >> Dear Gromacs Users, > > >> > > >> > > >> > > >> Recently when I tried to restart a md simulation from previous one > > >> using convert-tpr with version 5.0.1 , the task failed giving the > >> error > message: > > >> > > >> > > >> > > >> X particles communicated to PME node Y are more than a cell length > >> out > > >> of the domain decomposition cell of their charge group > > >> > > >> > > >> > > >> I tried several way to solve it, including modify the equilibration > > >> setting as it said in the gromacs error page, and all failed. If I > > >> just run one simulation for a long time, it will not crash, at > >> least > > >> can do further than the time point it crashed when using restart. > > >> > > >> Does anyone have any idea why this happen and how to solve it? I > >> used > > >> the > > >> syntax: > > >> > > >> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o > >> output.tpr > > >> -extend > > >> 1 > > >> > > >> Any suggestion will be greatly appreciated > > >> > > > > >Do not supply .trr and .edr files; just increase the number of steps > >and > continue from the existing checkpoint with mdrun -cpi. What you're > doing is based on ancient syntax that is no longer relevant. I'm > guessing that you're probably winding up with discontinuous states > somehow. > > > > > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Ver > sion_ > 4_and_Newer > > > > >-Justin > > > > Thank you so much for your timely reply, yet I tried mdrun -s > input.tpr -cpi input.cpt -append > > It still gave the same error message. Could it be a bug? Or I did > something wrong? Bug is possible but unlikely. We definitely don't have enough information to tell because we've gotten half of it each time - what was the conversion + restart combination you actually used? Does the original run stay + stable if it is not interrupted? Mark If I run a long time simulation continuously it can stay stable. I just want to run it in smaller jobs or restart it from a check point because of the limit on computing resources. Suggested by Justin I used syntax: mdrun -s input.tpr -cpi input.cpt -append, using the cpt file from the previous simulation yet it still gave the same error 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.
Re: [gmx-users] Gromacs 5.0.1 restart simulation
>> Dear Gromacs Users, >> >> >> >> Recently when I tried to restart a md simulation from previous one >> using convert-tpr with version 5.0.1 , the task failed giving the error message: >> >> >> >> X particles communicated to PME node Y are more than a cell length out >> of the domain decomposition cell of their charge group >> >> >> >> I tried several way to solve it, including modify the equilibration >> setting as it said in the gromacs error page, and all failed. If I >> just run one simulation for a long time, it will not crash, at least >> can do further than the time point it crashed when using restart. >> >> Does anyone have any idea why this happen and how to solve it? I used >> the >> syntax: >> >> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o output.tpr >> -extend >> 1 >> >> Any suggestion will be greatly appreciated >> >Do not supply .trr and .edr files; just increase the number of steps and continue from the existing checkpoint with mdrun -cpi. What you're doing is based on ancient syntax that is no longer relevant. I'm guessing that you're probably winding up with discontinuous states somehow. >http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_ 4_and_Newer >-Justin Thank you so much for your timely reply, yet I tried mdrun -s input.tpr -cpi input.cpt -append It still gave the same error message. Could it be a bug? Or I did something wrong? -- 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 5.0.1 restart simulation
Dear Gromacs Users, Recently when I tried to restart a md simulation from previous one using convert-tpr with version 5.0.1 , the task failed giving the error message: X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group I tried several way to solve it, including modify the equilibration setting as it said in the gromacs error page, and all failed. If I just run one simulation for a long time, it will not crash, at least can do further than the time point it crashed when using restart. Does anyone have any idea why this happen and how to solve it? I used the syntax: gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o output.tpr -extend 1 Any suggestion will be greatly appreciated -- 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] pdb2gmx cannot generate the right residue and atom numbers
Thank you for your reply. I am just wondering is there anyway we can make pdb2gmx change the default digit number? I am doing a membrane protein, and I already have a ideal model as a pdb file. If I need to go over the solvate(or genbox in the 4.5.x version), by default waterbox setting the water will go into the lipid layer since the algorithm is just to put water into all the spaces, I may have to manually delete those water. If I can just transfer the model it will make life much easier and I can also compare with the known result. Thanks again for your time! >In addition to what Joao said, the fixed-width .pdb format is fundamentally >unsuited to large systems. You need to find a way to avoid using such a >.pdb file as input to pdb2gmx; either solvate later, or use a different >format for input. > >Mark > > >On Mon, Aug 4, 2014 at 11:09 PM, WH wrote: > >> Dear Gromacs users, >> >> I want to use Gromacs to process a system with more than 8 water >> moelcules. However, when use pdb2gmx to deal the the pdb file, the out put >> .gro file has the form like this: >> 3409HOHHW234995 -5.617 -6.883 -8.771 >> 3409HOH OW34996 -6.108 -6.959 -7.760 >> 3409HOHHW134997 -6.107 -6.973 -7.855 >> 3409HOHHW234998 -6.199 -6.971 -7.735 >> 3409HOH OW34999 -4.964 -8.455 -9.110 >> 3409HOHHW135000 -5.054 -8.441 -9.081 >> 3409HOHHW235001 -4.939 -8.372 -9.150 >> 3409HOH OW35002 -6.157 -7.576 -8.913 >> 3409HOHHW135003 -6.187 -7.499 -8.962 >> >> Only 4 digits will be used for the residue number and 5 for the atom >> number. Thus, the actual residue number and atom number cannot be written >> correctly and lead to failure for the MD simulation. >> Does anyone know how to fix this problem? I really appreciate it. -- 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] pdb2gmx cannot generate the right residue and atom numbers
Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- 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.
