Re: [gmx-users] angle constraints
Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- 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 -- Tarak -- 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
[gmx-users] g_clustsize
Dear Gromacs Users, I don't know what is the quantity of -cut in g_clustsize for different systems, exactly! May I ask you to help me, Please? Best Regards Sara -- 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
[gmx-users] What is The gromacs tutorial output files?
Dear all user, I'm a gromacs beginner and have a quick question. I installed gromacs 4.5.5 online on ubuntu12.04. How do I check that it is correctly installed? and, What is The gromacs tutorial output files? I could not get them tpr file. Please help me. -- 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
[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Thanks for that comment. I've another query during inflating step in Justin's tutorial. In my case, during the inflation, 4 lipids from the upper and 2 lipids from the lower leaflets were removed. Would there be a problem in this sort non-uniform deletion (I mean like 4 from upper and 4 from lower)? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999633.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Regarding all angle constraint and hybridisation problem
Sir, Sorry for missing the subject in previous mail and adding new content in the old mail. Thanks Sir, for your suggestions. Changing the parameters in PRODRG generated .itp file just solved the problem. The bond lengths and hybridisation remained the same. The problem was there. Read your reference too. Regards, Radhika -- 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] What is The gromacs tutorial output files?
To check it, please enter commands as below: #grompp_d or #mdrun some options appear and at the end you will get an error that .top file was not found! For the second question, if you don't get the .tpr file it means you have not generate a correct simulation( however I don't now what the exact reason is). The final outputs are: .trr , .tpr and .edr. Sincerely, Shima From: Ali Alizadeh ali.alizadehmoja...@gmail.com To: gmx-users@gromacs.org Sent: Tuesday, July 24, 2012 11:13 AM Subject: [gmx-users] What is The gromacs tutorial output files? Dear all user, I'm a gromacs beginner and have a quick question. I installed gromacs 4.5.5 online on ubuntu12.04. How do I check that it is correctly installed? and, What is The gromacs tutorial output files? I could not get them tpr file. Please help me. -- gmx-users mailing list gmx-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 -- 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] angle constraints
An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Richard On 24/07/2012 07:21, tarak karmakar tarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- 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 -- 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] angle constraints
On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakar tarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- 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 -- 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
[gmx-users] How to port the parmbsc0 correction to gromacs?
Dear GMX users, As parmbsc0 force field significantly improve the representation of alpha/gamma torsions in nucleic acid simulations,i thus want to use the combination of parm99sb+parmbsc0 in Gromacs that was frequently employed in recent publications. However, when i searched the whole forum, i can rarely find any hints for how to do this. Could someone be so kindly to give me a step-by-step guide for the porting parmbsc0 corrections to a exsiting AMBER forcefiled (such as parm99sb) in Gromacs? Thanks in adcance! Best regards! Xiangqian Kong -- 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
[gmx-users] How to constrain some angles?
Dear gmxers, For some purpose, I want to constrain some angles. Note that it is some but not all, and constrain but not restrain. How to do with it? Thanks a lot for any reply. Chaofu Wu -- 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] How to constrain some angles?
On 24/07/2012 6:42 PM, Wu Chaofu wrote: Dear gmxers, For some purpose, I want to constrain some angles. Note that it is some but not all, and constrain but not restrain. How to do with it? As discussed earlier today on the list, you need to use a triangle of bond constraints to constrain an angle, and there are some cases where using virtual sites is best. 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] How to port the parmbsc0 correction to gromacs?
On 24/07/2012 6:47 PM, ÏéÇ« ¿× wrote: Dear GMX users, As parmbsc0 force field significantly improve the representation of alpha/gamma torsions in nucleic acid simulations,i thus want to use the combination of parm99sb+parmbsc0 in Gromacs that was frequently employed in recent publications. You will likely be best served contacting them to see if you can have access to their .itp files. However, when i searched the whole forum, i can rarely find any hints for how to do this. Could someone be so kindly to give me a step-by-step guide for the porting parmbsc0 corrections to a exsiting AMBER forcefiled (such as parm99sb) in Gromacs? If you don't succeed with the above, then you'll likely need to do your own legwork, looking at the functional forms implemented in parmbsc0 and available in GROMACS (see manual). Understanding of parts of chapters 4 and 5 of the manual will be required either way. 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] angle constraints
Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ? On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakar tarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- 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 -- 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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
[gmx-users] converting Desmond trajectories to Gromacs
Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] Re: Error in Membrane simulations with POPC bilayer
On 7/24/12 2:49 AM, J Peterson wrote: Thanks for that comment. I've another query during inflating step in Justin's tutorial. In my case, during the inflation, 4 lipids from the upper and 2 lipids from the lower leaflets were removed. Would there be a problem in this sort non-uniform deletion (I mean like 4 from upper and 4 from lower)? In principle, no. It sounds like you have an asymmetric protein, which thus requires an asymmetric modification to the bilayer. -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] converting Desmond trajectories to Gromacs
On 7/24/12 6:13 AM, Nidhi Jatana wrote: Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? The area per lipid is not a trivial quantity to calculate when there's a protein involved, and there is no Gromacs tool that will do it. We created a program a few years ago that does, but note that you cannot analyze a trajectory, only a single coordinate file (.gro or .pdb). The current workaround is to dump out a series of coordinate files and loop over all of them in a shell script. Note that, depending on how many frames you have in your trajectory, this may take quite a while - APL calculations typically take on the order of 2-5 minutes (per frame), depending on how large the system is. http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ -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] g_clustsize
On 7/24/12 2:34 AM, mohammad agha wrote: Dear Gromacs Users, I don't know what is the quantity of -cut in g_clustsize for different systems, exactly! It is the cutoff value that determines if two molecules are in the same cluster. If atoms in different molecules have a distance less than the value specified in -cut, they are in the same cluster. -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
[gmx-users] Re: angle constraints
As others said: type 2 virtual site check chapter 4.7 and 5.2.2 in the manual (version 4.5.x). Greetings Thomas Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org: Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ? On Tue, Jul 24, 2012 at 2:06 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakartarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website athttp://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- gmx-users mailing listgmx-us...@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 togmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-us...@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 togmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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
[gmx-users] Bins in wham analysis
Dear Gromacs users, I have a query regarding the number of bins used in wham analysis. If I have performed by simulations over 15 umbrellas (15 different staring structures), what should be the ideal number of bins to perform wham analysis? Does it depend on the number of umbrellas. For example: 1) Should I use more than 15 bins in my case, and the one that gives proper overlap in histogram ? 2) Or any number of bins (even if it is less than 12) can be used, if I get proper overlap in my histogram output? Any suggestion is appreciated. -- Thanks and regards, Neeru Sharma -- 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
[gmx-users] Re: Issue with GROMACS file format
Thanks Justin for your reply. Going by the Gromacs file format: position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) It is not clear to me as to how many digits before the decimal point can a coordinate column accepts in the Gro file- Is it 3 or 4 digits before the decimal point? (If it is 3 digits before the decimal then there should be a white space between coordinate columns.) Thanks, Satya. -- View this message in context: http://gromacs.5086.n6.nabble.com/Issue-with-GROMACS-file-format-tp4999612p4999649.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Issue with GROMACS file format
On 7/24/12 8:18 AM, SatyaK wrote: Thanks Justin for your reply. Going by the Gromacs file format: position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) It is not clear to me as to how many digits before the decimal point can a coordinate column accepts in the Gro file- Is it 3 or 4 digits before the decimal point? (If it is 3 digits before the decimal then there should be a white space between coordinate columns.) Theoretically, the .gro format can accept 4 digits before the decimal point (8 total columns, 3 used for after the decimal and one for the decimal point, which leaves 4). The problem in your case is that VMD does not correctly parse the value even though it is technically acceptable within Gromacs. One normally does not deal with coordinates on the order of 1000 nm, so whoever wrote the VMD plugin for changing coordinate file formats probably didn't account for that. -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
[gmx-users] Calculation of Spectroscopic properties
Dear gmx-users I am trying to calculate the optical rotation of a molecule in solution. There are several examples of this in the literature where they take snapshots of molecule at intervals throughout the trajectory, calculate optical rotation, and average them to get a solvated optical rotation. I have tried using this method by my numbers don't seem to converge on any one value, for example over 6ns trajectory, using 3000 snapshots I get a calculated rotatory power of ~20 deg/cm average with a standard deviation 745 deg/cm! (calculated with atom-dipole interaction model). my molecule does have a long carbon chain which may be the problem. So would it help to pick out the most common configurations and do calculations on them perhaps? is there a feature of gromacs that will determine the most probable conformations? Also I set up an single point energy calculation of each snapshot using mdrun -rerun (but this is on the unsolvated molecule) for possible comparison of the snapshot energies, but is there a better way of getting these energies from the energy file? Thanks in advance for any responses Cody Covington -- 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
[gmx-users] Re: g_clustsize
Please keep the discussion on the gmx-users list. On 7/24/12 8:31 AM, mohammad agha wrote: Dear Justin, Thank you very much from your response, is there only RDF calculations to reach cutoff value? RDF is one possible method to find out how closely atoms or molecules are interacting, but it may get a bit muddled if the molecules are rather complex or sample many conformations. -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
[gmx-users] dendrimer simulation
I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands with peptide oligomers. I have succesfully generated the .itp file needed, and have run some simulation. The same applies to the peptide. However i run into problems combining them. It appears the specbond.dat file is only applied when invoking pdb2gmx, but my dendrimer is not added to the .rtp database, so pdb2gmx fails. (The peptide is bonded through a disulfide like bond to the dendrimer.) Is there an option to directly linking the denrimer and the peptide in the topology files? (the dendrimer utilises GAFF parameters, and they are only present in the .itp file, i dont especialy want to extend the regular force field with these parameters). Any suggestions are appreciated Lekacs Nemeth -- 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] dendrimer simulation
On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote: I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands with peptide oligomers. I have succesfully generated the .itp file needed, and have run some simulation. The same applies to the peptide. However i run into problems combining them. It appears the specbond.dat file is only applied when invoking pdb2gmx, but my dendrimer is not added to the .rtp database, so pdb2gmx fails. (The peptide is bonded through a disulfide like bond to the dendrimer.) Is there an option to directly linking the denrimer and the peptide in the topology files? (the dendrimer utilises GAFF parameters, and they are only present in the .itp file, i dont especialy want to extend the regular force field with these parameters). You cannot create bonds between molecules in separate [moleculetype] blocks. Thus, if your molecules are in separate .itp files, you cannot create the necessary bonds. For branched molecules, the only way to have such linkages is to create .rtp entries and use specbond.dat. -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] dendrimer simulation
Thank you for the fast answer, i will do that then. Do i have to close this thread, or it will fade by itself? Lukacs On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote: I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands with peptide oligomers. I have succesfully generated the .itp file needed, and have run some simulation. The same applies to the peptide. However i run into problems combining them. It appears the specbond.dat file is only applied when invoking pdb2gmx, but my dendrimer is not added to the .rtp database, so pdb2gmx fails. (The peptide is bonded through a disulfide like bond to the dendrimer.) Is there an option to directly linking the denrimer and the peptide in the topology files? (the dendrimer utilises GAFF parameters, and they are only present in the .itp file, i dont especialy want to extend the regular force field with these parameters). You cannot create bonds between molecules in separate [moleculetype] blocks. Thus, if your molecules are in separate .itp files, you cannot create the necessary bonds. For branched molecules, the only way to have such linkages is to create .rtp entries and use specbond.dat. -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 -- 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] dendrimer simulation
On 7/24/12 10:39 AM, neme...@pharm.u-szeged.hu wrote: Thank you for the fast answer, i will do that then. Do i have to close this thread, or it will fade by itself? Nothing fades, everything stays archived :) But if the issue is closed, simply stop replying to the thread, and ask any new questions in the future by sending a new mail. -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] Re: angle constraints
How to choose the positions of the dummy atoms while constraining the angle for a linear triatomic molecule? The topology for a such molecule ( af for example CO2 ) is as follows [ moleculetype ] ; Namenrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 503 CO rtp CO q 0.0 1 D1503 CO D1 1 0 21.90158 ; qtot 0 2 D2503 CO D2 2 0 21.90158 ; qtot 0 3 CE503 CO CO 30.7 0.0 ; qtot 0.7 4 OE503 COOC1 4 -0.35 0.0 ; qtot 0.35 5 OE503 COOC2 5 -0.35 0.0 ; qtot 0.35 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 The .rtp file for CO2 [ CO ] [ atoms ] D1 D1 0. 1 D2 D2 0. 2 COCE 0.70003 OC1 OE -0.3500 4 OC2 OE -0.3500 5 [ bonds ] COOC1 COOC2 Can anyone please check above file parts whether I'm doing correct or not ? On Tue, Jul 24, 2012 at 4:25 PM, Thomas Schlesier schl...@uni-mainz.de wrote: As others said: type 2 virtual site check chapter 4.7 and 5.2.2 in the manual (version 4.5.x). Greetings Thomas Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org: Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ? On Tue, Jul 24, 2012 at 2:06 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakartarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website athttp://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- gmx-users mailing listgmx-us...@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 togmx-users-requ...@gromacs.org. * Can't post?
