Re: [gmx-users] g_wham problem with negative COM differences
Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thank's! I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull= umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. Such changes do not seem appropriate to me. If you change the sign of the pulling force, you change the implication of what that value means. What happens if you run your simulations with the new (more appropriate) .mdp file? Do the forces have the same magnitude, but opposite sign? I don't think that the problem is so easy fixed. I had with another person about a month ago a lengthy discussion on the list. The problem is the following: If you use 'distance' as pull_geometry the position of the minimum of the umbrella potential is determined by the vector connecting the ref- and pulled group, but there is no information about the direction
Re: [gmx-users] g_wham problem with negative COM differences
Anni Kauko wrote: Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thank's! I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull= umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half
Re: Re: [gmx-users] g_wham problem with negative COM differences
Date: Wed, 11 Apr 2012 08:38:05 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f857b2d.3050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thank's! I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull= umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. -Anni PS. Thank's for your excellent tutorials. They have been indispensable help for me to get started with gromacs! -- Anni Kauko, Ph.D. Post Doctoral Researcher Structural Bioinformatics Laboratory Dept. of Biosciences, Biochemistry Åbo Akademi University 20520 Turku, Finland phone: +358 (0)2 215 4006 mobile: +358 (0)50-576 8656 -- 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] g_wham problem with negative COM differences
Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thank's! I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull= umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. Such changes do not seem appropriate to me. If you change the sign of the pulling force, you change the implication of what that value means. What happens if you run your simulations with the new (more appropriate) .mdp file? Do the forces have the same magnitude, but opposite sign? -Anni PS. Thank's for your excellent tutorials. They have been indispensable help for me to get started with gromacs! Glad to hear it :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] g_wham problem with negative COM differences
New try, think last time message didn't reached the list :( Original-Nachricht Betreff: Re: g_wham problem with negative COM differences Datum: Fri, 13 Apr 2012 14:55:15 +0200 Von: Thomas Schlesier schl...@uni-mainz.de An: gmx-users@gromacs.org Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4f857b2d.3050...@vt.edu mailto:4f857b2d.3050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thank's! I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull= umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol-1 nm-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. Such changes do not seem appropriate to me. If you change the sign of the pulling force, you change the implication of what that value means. What happens if you run your simulations with the new (more appropriate) .mdp file? Do the forces have the same magnitude, but opposite sign? I don't think that the problem is so easy fixed. I had with another person about a month ago a lengthy discussion on the list. The problem is the following: If you use 'distance' as pull_geometry the position of the minimum of the umbrella potential is determined by the vector connecting the ref- and pulled group, but there is no information about
[gmx-users] g_wham problem with negative COM differences
Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 I would appreciate help very much. -Anni -- Anni Kauko, Ph.D. Post Doctoral Researcher Structural Bioinformatics Laboratory Dept. of Biosciences, Biochemistry Åbo Akademi University 20520 Turku, Finland phone: +358 (0)2 215 4006 mobile: +358 (0)50-576 8656 -- 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] g_wham problem with negative COM differences
Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0. 6.26031 2.27369 pullz_umbr_23.xvg: 0. 6.09702 0.0233141 pullz_umbr_50.xvg: 0. 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha__r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 Your problem stems from the use of distance geometry. This method assumes the sign along the reaction coordinate does not change, i.e. always positive or always negative. If the sign changes, this simple method fails. You should be using something like position to allow for a vector to be specified. Perhaps you can reconstruct the PMF by separately analyzing the positive restraint distances and negative restraint distances (note here that distance really refers to a vector quantity, and thus it can have a sign), or otherwise create new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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: [gmx-users] g_wham problem
Oh, that would be convenient. Thanks. --- 09年8月3日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] g_wham problem 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年8月3日,周一,上午9:01 accomp lin wrote: Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn mailto:accomp...@student.dlut.edu.cn The Gromacs 4.0.x series contains a fixed g_wham that can handle the .pdo output of Gromacs 3.3.x. Using this official version might make it easier to get technical support, should you need it. -Justin Thanks a lot Jiaqi 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ 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! 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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! 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 ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ 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_wham problem
Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn Thanks a lot Jiaqi ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ 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
Re: [gmx-users] g_wham problem
accomp lin wrote: Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn mailto:accomp...@student.dlut.edu.cn The Gromacs 4.0.x series contains a fixed g_wham that can handle the .pdo output of Gromacs 3.3.x. Using this official version might make it easier to get technical support, should you need it. -Justin Thanks a lot Jiaqi 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
