Re: Fw: [gmx-users] water molecule can not be settled
I thought the sole purpose of open source discussions and sharing is to help any scientific (or other) community to grow and benefit from each other, without taking into account the Nationality of the beneficiaries. If someone is willingly helping out somebody, whether Indian or not, in the GROMACS forum, then it should not bother Mr. Luis Felipe Pineda de Castro, since to the best of my knowledge it is not affecting him. I would request the moderators of this forum to take adequate measures about such postings as Mr. Castro's. Regards, Anirban On Fri, Apr 5, 2013 at 10:55 PM, Luis Felipe Pineda de Castro < luis.pinedadecas...@lnu.se> wrote: > After having followed for longer time the queries sent by some Indian > fellows, I wonder if it wouldn't more effective to arrange for a GROMACS > tutorial offered by Justin in an Indian location. Maybe you, the Indian > fellows, can arrange for the financing and invite Justin to hold such a > Tutorial on the basics of MD simulations and their implementation in > GROMACS. Considering the time Justin is spending responding to your > queries, maybe because you are devoid of adequate supervision or > theoretical background, this would be only fair. This posting is maybe a > little bit off topic, but somehow related. > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] > Sent: Friday, April 05, 2013 5:22 PM > To: Discussion list for GROMACS users > Subject: Re: Fw: [gmx-users] water molecule can not be settled > > You mean start over the NPT step? > > > > Sincerely, > Shima > > > - Original Message - > From: Justin Lemkul > To: Discussion list for GROMACS users > Cc: > Sent: Friday, April 5, 2013 7:50 PM > Subject: Re: Fw: [gmx-users] water molecule can not be settled > > On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh > wrote: > > > As I visualized the system, I see a water molecule somewhere between > lipid > > chains near the protein entrance. This has been happen during NPT. I' d > > like to delete this molecule but with such a kind of fatal error this > would > > impossible. So what's the way? Is there any tricky way to change > > coordinate of molecule? but I seems also impossible becasue PME problem! > > So whats the solution? > > > > > Delete the molecule, adjust your topology (and index file, if necessary), > and start over with the equilibration. > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > -- > 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: Fw: [gmx-users] water molecule can not be settled
After having followed for longer time the queries sent by some Indian fellows, I wonder if it wouldn't more effective to arrange for a GROMACS tutorial offered by Justin in an Indian location. Maybe you, the Indian fellows, can arrange for the financing and invite Justin to hold such a Tutorial on the basics of MD simulations and their implementation in GROMACS. Considering the time Justin is spending responding to your queries, maybe because you are devoid of adequate supervision or theoretical background, this would be only fair. This posting is maybe a little bit off topic, but somehow related. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Friday, April 05, 2013 5:22 PM To: Discussion list for GROMACS users Subject: Re: Fw: [gmx-users] water molecule can not be settled You mean start over the NPT step? Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. So what's the way? Is there any tricky way to change > coordinate of molecule? but I seems also impossible becasue PME problem! > So whats the solution? > > Delete the molecule, adjust your topology (and index file, if necessary), and start over with the equilibration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 11:22 AM, Shima Arasteh wrote: > You mean start over the NPT step? > > Yes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Fw: [gmx-users] water molecule can not be settled
You mean start over the NPT step? Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. So what's the way? Is there any tricky way to change > coordinate of molecule? but I seems also impossible becasue PME problem! > So whats the solution? > > Delete the molecule, adjust your topology (and index file, if necessary), and start over with the equilibration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. So what's the way? Is there any tricky way to change > coordinate of molecule? but I seems also impossible becasue PME problem! > So whats the solution? > > Delete the molecule, adjust your topology (and index file, if necessary), and start over with the equilibration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Fw: [gmx-users] water molecule can not be settled
As I visualized the system, I see a water molecule somewhere between lipid chains near the protein entrance. This has been happen during NPT. I' d like to delete this molecule but with such a kind of fatal error this would impossible. So what's the way? Is there any tricky way to change coordinate of molecule? but I seems also impossible becasue PME problem! So whats the solution? Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, April 5, 2013 7:42 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh wrote: I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? > > It's unlikely that some ad hoc change will magically fix a problem. Energy minimization should take care of clashes. Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. > > Right, because you've now changed the contents of the system. It no longer matches the topology and the trajectory would then be discontinuous. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh wrote: > I' d like to know if it is acceptable to change the molecule coordinates > to solve this problem? > > It's unlikely that some ad hoc change will magically fix a problem. Energy minimization should take care of clashes. > Some time back, I deleted such a molecule and then I got a fatal error > containing that the trj file and other inputs are not inconsistent. > > Right, because you've now changed the contents of the system. It no longer matches the topology and the trajectory would then be discontinuous. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Fw: [gmx-users] water molecule can not be settled
I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. Would you please give me suggestions? I need them urgently. I really appreciate your help. Sincerely, Shima - Forwarded Message - From: Shima Arasteh To: Discussion list for GROMACS users Sent: Friday, April 5, 2013 6:25 PM Subject: [gmx-users] water molecule can not be settled Hi all, I am trying to simulate a system of protein and lipid bilayer ( in this case POPC). The ff I am using is CHARMM36 and I used related settings from literature. I used InflateGRO to pack the lipids around my protein. Then put a position restraint on my protein and P atoms of POPC. With these position restraints I ran NVT for 1ns and NPT for around10 ns. ( I need to say that NPT has been done in three steps: 1.First 5ns with position restraint on whole protein and P atoms 2. Then 3 ns with position restraint on just protein atoms 3. And finally 1 ns with position restraint on protein without H atoms. ) In fact, I tried to prevent any crash by sudden changes. Next, I tried to run MDRUN, but I get the error of "some water molecules can not be settled". This means that my system has not been equiliberated sufficiently. OK, what should I do? How can I solve it? Water molecules can not be deleted in this step because I will get another fatal error as a result. My system seems fine. The pressure and energy plots don't show anything unusual. But I dont know how can I solve the problem. Would you please give me any suggestions? Reducing the timestep and also changing the thermostat could not help my system to overcome this problem. What would be the best solution? Sincerely, Shima -- 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
