[gmx-users] Different values of area per lipid with/without protein
Hi all I embedded the protein in POPC using inflategro. After the desired area per lipid (APL-0.64 A2) is reached I recalculated the APL with and without the protein. I get two different values; with the protein - 0.64 and without the protein - 0.82. I ran perl inflategro input.gro 1 POPC 0 output.gro 5 area.dat to get the above values. I was expecting to get the same values for the two cases. Can someone explain the reason for this difference, since inflategro subtract the area of the protein in any case. The size of the system is 6.5 6.5 7.5. Thank you -- 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: Re: g_rmsf reference structure? (Tsjerk Wassenaar)
Thank you very much for the clarification! Message: 1 Date: Wed, 16 Feb 2011 10:46:18 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] g_rmsf reference structure? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTi=6-rmt6k+kz1+qpfsa-ottgfpiry5+eppv+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. 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 -- 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! End of gmx-users Digest, Vol 82, Issue 126 ** -- 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] g_rmsf reference structure?
Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? Thanking in advance for clarification. -- 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] homology modelling workshop?
Dear All, This question is off from the regular questions of Gromacs but I hope some of you would be able to help me. I wish to know whether there is any homology modelling workshop organized anywhere, during the rest of this year. It would be greatly appreciated if any of you can give me an update. Thanking you in advance kulleperuma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 18
Quoting gmx-users-requ...@gromacs.org: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: g_principal: memory corruption (David van der Spoel) -- Message: 1 Date: Sat, 03 Jul 2010 09:36:58 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_principal: memory corruption To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c2ee89a.2070...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2010-07-03 02.40, kulleperuma.kulleper...@utoronto.ca wrote: Hi all, I am using Gromacs-4.0.5 g_principal for a system with a protein of 132 resiudes, ~450 octane molecules and ~9000 water molecules, as below, g_principal -f pos_Rep.xtc -s em.tpr -n index.ndx (Protein was the selected group ). I get the follwing message soon after I selected Protein Reading frame 0 time 0.000 *** glibc detected *** g_principal: malloc(): memory corruption: 0x0646c250 *** === Backtrace: = /lib64/libc.so.6[0x2b4788cd24ac] /lib64/libc.so.6(__libc_calloc+0xc0)[0x2b4788cd3ce0] g_principal[0x41071c] g_principal[0x471aff] g_principal[0x472237] g_principal[0x410539] g_principal[0x40251f] g_principal[0x402139] /lib64/libc.so.6(__libc_start_main+0xf4)[0x2b4788c7d974] g_principal[0x402079] === Memory map: . This error didn't occur and ran smoothly when .gro file was selected for -f flag, but failed even for a shorter trajectory file. What is the way around for this problem Thank you in advance! Please submit a bugzilla with a short trajectory (since it crashes at time 0 one frame is enough). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- 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/search before posting! End of gmx-users Digest, Vol 75, Issue 18 * Thank you David and sorry for the late reply, The problem is fixed. It's my mistake, I have been using a xtc file from a position restrained equilibration, where the protein was fixed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_principal: memory corruption
Hi all, I am using Gromacs-4.0.5 g_principal for a system with a protein of 132 resiudes, ~450 octane molecules and ~9000 water molecules, as below, g_principal -f pos_Rep.xtc -s em.tpr -n index.ndx (Protein was the selected group ). I get the follwing message soon after I selected Protein Reading frame 0 time0.000 *** glibc detected *** g_principal: malloc(): memory corruption: 0x0646c250 *** === Backtrace: = /lib64/libc.so.6[0x2b4788cd24ac] /lib64/libc.so.6(__libc_calloc+0xc0)[0x2b4788cd3ce0] g_principal[0x41071c] g_principal[0x471aff] g_principal[0x472237] g_principal[0x410539] g_principal[0x40251f] g_principal[0x402139] /lib64/libc.so.6(__libc_start_main+0xf4)[0x2b4788c7d974] g_principal[0x402079] === Memory map: . This error didn't occur and ran smoothly when .gro file was selected for -f flag, but failed even for a shorter trajectory file. What is the way around for this problem Thank you in advance! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
