RE: [gmx-users] trjconv and -pbc
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan wrote: > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of lina [lina.lastn...@gmail.com] > Sent: Thursday, October 27, 2011 10:47 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] trjconv and -pbc > > Hi, > > I have a problem using > > trjconv_g -pbc nojump > or > > trjconv_g -pbc nojump -center > > I even tried the -pbc whole. > > The system is protein with a small molecular, for the first time > period, when I checked on pymol. > they are together, but later they apart, after show cell, protein > inside the cell, while this small molecular outside, > > I did not meet such issue before, it's used to be easy to fix the pbc > problem, but not this one. a bit surprise, > > They are supposed to be together, > > Thanks for any advice, > > > > I am sure it will help. Follow the workflow! > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc > > Just use the trjconv -h to see each option. Ha, I think I have tried those options. That's why I am confused. Thanks, > > Jan > > === > Jan Marzinek > PhD Candidate > Centre for Process Systems Engineering > Department of Chemical Engineering > Imperial College London > South Kensington Campus > London SW7 2AZ > E: j.marzine...@imperial.ac.uk > M: +44(0)7411 640 552 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On 28/10/2011 2:39 PM, lina wrote: On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Ha, I think I have tried those options. That's why I am confused. Thanks, Well, you need to try them better :) If you want your trajectory to keep protein and something else together, you will need an index group that combines them not jumping, and then combines them centering (or whatever). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
Hi Lina, Make sure to use a reference in which the molecules are together (clustered) the way you want them. Cheers, Tsjerk On Oct 27, 2011 11:47 AM, "lina" wrote: Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham wrote: > On 28/10/2011 2:39 PM, lina wrote: >> >> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan >> wrote: >>> >>> >>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on >>> behalf of lina [lina.lastn...@gmail.com] >>> Sent: Thursday, October 27, 2011 10:47 AM >>> To: Discussion list for GROMACS users >>> Subject: [gmx-users] trjconv and -pbc >>> >>> Hi, >>> >>> I have a problem using >>> >>> trjconv_g -pbc nojump >>> or >>> >>> trjconv_g -pbc nojump -center >>> >>> I even tried the -pbc whole. >>> >>> The system is protein with a small molecular, for the first time >>> period, when I checked on pymol. >>> they are together, but later they apart, after show cell, protein >>> inside the cell, while this small molecular outside, >>> >>> I did not meet such issue before, it's used to be easy to fix the pbc >>> problem, but not this one. a bit surprise, >>> >>> They are supposed to be together, >>> >>> Thanks for any advice, >>> >>> >>> >>> I am sure it will help. Follow the workflow! >>> >>> >>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc >>> >>> Just use the trjconv -h to see each option. >> >> Ha, I think I have tried those options. That's why I am confused. >> >> Thanks, > > Well, you need to try them better :) If you want your trajectory to keep > protein and something else together, you will need an index group that > combines them not jumping, and then combines them centering (or whatever). Thanks. I did use the index group on trjconv to output the pdb of the protein and the small molecular. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Make sure to use a reference in which the molecules are together (clustered) > the way you want them. I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. > > Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, > > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" wrote: > > Hi, > > I have a problem using > > trjconv_g -pbc nojump > or > > trjconv_g -pbc nojump -center > > I even tried the -pbc whole. > > The system is protein with a small molecular, for the first time > period, when I checked on pymol. > they are together, but later they apart, after show cell, protein > inside the cell, while this small molecular outside, > > I did not meet such issue before, it's used to be easy to fix the pbc > problem, but not this one. a bit surprise, > > They are supposed to be together, > > Thanks for any advice, > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Tsjerk On Oct 28, 2011 6:27 AM, "lina" wrote: On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Make su... I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. > > Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, > > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" wrote: > > Hi, > > I have ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] trjconv and -pbc
-pbc atom Date: Fri, 28 Oct 2011 06:34:28 +0200 Subject: Re: [gmx-users] trjconv and -pbc From: tsje...@gmail.com To: gmx-users@gromacs.org Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Tsjerk On Oct 28, 2011 6:27 AM, "lina" wrote: On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Make su...I used the initial mdrun .tpr. After checking the generated pdb > (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. > > Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, > > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" wrote: > > Hi, > > I have ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 > > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" wrote: > > On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar > wrote: > Hi Lina, > > Make su... > > I used the initial mdrun .tpr. After checking the generated pdb (total > 51 frames), the first 28/29 frames both are together, but later are > separated. (the intra_fit also not work as expected). > > So I think at beginning the reference initial ones are together. > > This .xtc were trjcat together, first 200ns and then extend to 500ns, > the .pdb generated used dt 10ns. >> >> Cheers, > Am I wrong in some places? Actually for other trajectories I had no > problem (use the same way of handling it). > > Thanks, > >> > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" >> > wrote: > > Hi, > > I have ... > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, "lina" wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 > > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" wrote: > > On Fri, Oct 28... > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/g... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? Cheers, Tsjerk On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Don't combine fitting, centering and pbc options. It may not work as > expected. That's why the workflow is given. Use separate passes. By the way, > first centering on the protein followed by putting molecules in the box > should also work. > > Cheers, > > Tsjerk > > On Oct 28, 2011 9:01 AM, "lina" wrote: > > On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar > wrote: > Hi Lina, > > >> Try a _translational_ fit on the protein, follwed by a pass with -pbc >> nojump > > Hope it helps, > > Hi, > > Thanks. > > I tried trjconv_g -fit translation -pbc nojump, ideally it should work. > > but still not, > > after I tried the minidist, I noticed the peak around 270ns, > > I attached the figure, what's the possible reason for this distance? > > Thanks, > > P.S the box dimension 6.21279 6.21279 6.21279 > >> > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" >> > wrote: > > On Fri, Oct 28... > >> -- > gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/g... > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > My previous reply was from before I looked at the graph. Have you > considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! > or goes to another side of the protein? Have you looked at the > trajectory, in particular at the trajectory with the jumps removed? I extracted the parts from 280ns to 300ns, the presentation of that part protein is not whole. In the former way, the time since 280ns till the end, the small molecular still outside the cell/box. even the minidist is very small later. I am not sure how to get the trajectory and view? (ngmx? ) > Thanks, > Cheers, > > Tsjerk > > On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar wrote: >> Hi Lina, >> >> Don't combine fitting, centering and pbc options. It may not work as >> expected. That's why the workflow is given. Use separate passes. By the way, >> first centering on the protein followed by putting molecules in the box >> should also work. >> >> Cheers, >> >> Tsjerk >> >> On Oct 28, 2011 9:01 AM, "lina" wrote: >> >> On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar >> wrote: > Hi Lina, > >> >>> Try a _translational_ fit on the protein, follwed by a pass with -pbc >>> nojump > > Hope it helps, >> >> Hi, >> >> Thanks. >> >> I tried trjconv_g -fit translation -pbc nojump, ideally it should work. >> >> but still not, >> >> after I tried the minidist, I noticed the peak around 270ns, >> >> I attached the figure, what's the possible reason for this distance? >> >> Thanks, >> >> P.S the box dimension 6.21279 6.21279 6.21279 >> >>> > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" >>> > wrote: > > On Fri, Oct 28... >> >>> -- > gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/g... >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
Hi Lina, You first remove the jumps from the trajectory. Then you can view that trajectory with ngmx or with VMD. You can also then extract the frames around the 'jump' and look at them. But if the molecule goes unstuck and then crosses the boundary to get stuck to the protein again, it would give exactly that result: Visually, the molecule seems close, goes away and apparently gets stuck somewhere floating nowhere. But the minimal distance to the protein would be really minimal then go through a maximum and go to the minimal level again. Cheers, Tsjerk On Fri, Oct 28, 2011 at 12:31 PM, lina wrote: > On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar wrote: >> Hi Lina, >> >> My previous reply was from before I looked at the graph. Have you >> considered that the molecule might be taking a stroll and turn back, > Ha ... stroll?! >> or goes to another side of the protein? Have you looked at the >> trajectory, in particular at the trajectory with the jumps removed? > > I extracted the parts from 280ns to 300ns, the presentation of that > part protein is not whole. > > In the former way, the time since 280ns till the end, the small > molecular still outside the cell/box. even the minidist is very small > later. > > I am not sure how to get the trajectory and view? (ngmx? ) >> > > Thanks, >> Cheers, >> >> Tsjerk >> >> On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar wrote: >>> Hi Lina, >>> >>> Don't combine fitting, centering and pbc options. It may not work as >>> expected. That's why the workflow is given. Use separate passes. By the way, >>> first centering on the protein followed by putting molecules in the box >>> should also work. >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Oct 28, 2011 9:01 AM, "lina" wrote: >>> >>> On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar >>> wrote: > Hi Lina, > >>> Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, >>> >>> Hi, >>> >>> Thanks. >>> >>> I tried trjconv_g -fit translation -pbc nojump, ideally it should work. >>> >>> but still not, >>> >>> after I tried the minidist, I noticed the peak around 270ns, >>> >>> I attached the figure, what's the possible reason for this distance? >>> >>> Thanks, >>> >>> P.S the box dimension 6.21279 6.21279 6.21279 >>> > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" > wrote: > > On Fri, Oct 28... >>> -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/g... >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: RE: [gmx-users] trjconv and -pbc
Vijaya, Can you explain how you think that may help solve the problem? I think it won't. Tsjerk On Oct 28, 2011 7:40 AM, "vijaya subramanian" wrote: -pbc atom -- Date: Fri, 28 Oct 2011 06:34:28 +0200 Subject: Re: [gmx-users] trjconv and -pbc From: tsje...@gmail.com To: gmx-users@gromacs.org Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it help... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
