Re: [gmx-users] grommp warning
Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right As per your answer in these archieve... http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html Under NPT the box size changes each step. You are using position restraints to a pre-defined set of reference coordinates. This option allows you to choose how those *reference coordinates* should change when the box size changes (respectively do not scale them at all, scale them all, or scale their COM but leave their internal geometry fixed). Position restraints are then applied using the updated reference coordinates. In some archives I found if any one used freeze group suggested to use refcoord_scaling = no When we applied position restrain, the position of backbone atom is restrained.. I make my assumption as like follow.. No = no scalling in position of atoms.(system maintain rigidity). all = the system bcome flexible com= ? ( scalling com means changing com co-ordinates or something else) I get confused Please accept my apology for stupid question Please help to come out through the confusion. With best wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
On 15/08/2012 4:52 PM, rama david wrote: Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right Probably. That's up to you. Only you know your overall objective about why you want to use PR and NPT. As per your answer in these archieve... http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html Under NPT the box size changes each step. You are using position restraints to a pre-defined set of reference coordinates. This option allows you to choose how those *reference coordinates* should change when the box size changes (respectively do not scale them at all, scale them all, or scale their COM but leave their internal geometry fixed). Position restraints are then applied using the updated reference coordinates. In some archives I found if any one used freeze group suggested to use refcoord_scaling = no When we applied position restrain, the position of backbone atom is restrained.. I make my assumption as like follow.. No = no scalling in position of atoms.(system maintain rigidity). all = the system bcome flexible com= ? ( scalling com means changing com co-ordinates or something else) There's a definition in manual 7.3... what else are you asking for? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really surprised by my observation With best wishes and regards Rama David.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
On 8/14/12 11:15 AM, rama david wrote: Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really surprised by my observation New features, bug fixes, and checks are introduced all the time. This particular check was introduced in September 2011, just before the release of 4.5.5, so you will not get the error when using 4.5.4. -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 * Only plain text messages are allowed! * 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] grommp warning
Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... With best wishes and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
On 8/14/12 11:28 AM, rama david wrote: Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... A simple search of the list archive turns up lots of discussions like this one: http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html -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 * Only plain text messages are allowed! * 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] grommp warning
Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to use refcoord_scaling no or all .?? Is there any way to find out which option to use when How all the things going to affect the result I goes trough archive but not find satisfactory answer... I am looking for clear and simple explanation... Thank you in advance.. With Best wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
On 15/08/2012 2:43 PM, rama david wrote: Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to use refcoord_scaling no or all .?? Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. Is there any way to find out which option to use when Thinking about it :-) How all the things going to affect the result I goes trough archive but not find satisfactory answer... I am looking for clear and simple explanation... Using position restraints ensures you do not reach the NPT ensemble. Whatever option you choose, you will need to simulate further without your position restraints to reach equilibrium. You should focus on minimizing the need for them, by making your system have the right density to start with. Then the volume change will be negligible, and the difference between these options likewise. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grommp warning
On 8/13/12 12:36 PM, Shima Arasteh wrote: Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? Yes, and there are several posts in the list archive explaining its origin, interpretation, and solution. The warning is : WARNING 1 [file NPT.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. You need to set a sensible value for the quoted option. Consult the manual and list archive. -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 * Only plain text messages are allowed! * 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] grommp warning
OK, thanks. But please let me know something: Is the pressure coupling with absolute position restraints is an option to fix a volume significantly? If yes, then It's me to think about keeping fix the volume of my system or not. Thanks, believe me I got this point through the mailing list :-) Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 14, 2012 12:08 AM Subject: Re: [gmx-users] grommp warning On 8/13/12 12:36 PM, Shima Arasteh wrote: Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? Yes, and there are several posts in the list archive explaining its origin, interpretation, and solution. The warning is : WARNING 1 [file NPT.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. You need to set a sensible value for the quoted option. Consult the manual and list archive. -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 * Only plain text messages are allowed! * 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] grommp warning
On 8/13/12 3:47 PM, Shima Arasteh wrote: OK, thanks. But please let me know something: Is the pressure coupling with absolute position restraints is an option to fix a volume significantly? If yes, then It's me to think about keeping fix the volume of my system or not. You can't have constant pressure and constant volume. If you don't set refcoord_scaling appropriately, you will have artifacts and potential instabilities. -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 * Only plain text messages are allowed! * 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
