[gmx-users] Hamiltonian REMD code uploaded in gromacs / user contributions / other software
Assist Prof. Yuguang Mu School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 Office: 04s-46 Tel: +65-63162885 Fax: +65-67913856 Email:y...@ntu.edu.sg CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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] Still model
Dear Chi-Xheng, We have tried GB module in gromacs, but unfortunately we found something wrong with it. What we found is that the results got from gromacs were quite different from those obtained from AMBER codes. We did not check in details why. Yuguang From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Chi-cheng Chiu Sent: Saturday, April 09, 2011 8:33 AM To: gmx-users@gromacs.org Subject: [gmx-users] Still model Hi all, I looked at source code in /src/mdlib/genborn.c and have two questions regarding the Still implicit solvent model. 1. in the function calc_gb_chainrule(), only Still model have extra factor of 2 apply on dvda, which I don't know why. 2. in calc_gb_rad_still(), does dccf miss a factor of 2? ( hope I did my math correct) Thanks in advance! Regard, Chi-xheng CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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] cvs version
Hi all, When I use cvs version, pdb2gmx, it shows such error Program pdb2gmx_cvs, VERSION 4.0.99-dev-20100328-954f577 Source code file: pdb2top.c, line: 137 Fatal error: No force fields found (files with name 'forcefield.itp' in subdirectories ending on '.ff') For more information and tips for trouble shooting please check the GROMACS website at http://www.gromacs.org/Documentation/Errors how to treat with? Yuguang CONFIDENTIALITY: This email is intended solely for the person(s) named. The contents may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us, and do not copy or use it, nor disclose its contents. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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] compiling problem
No, even I do not use mpi , the error is still there. Regards Yuguang From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yang Ye Sent: Wednesday, September 16, 2009 2:34 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] compiling problem Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sgmailto:y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.githttp://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ 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] compiling problem
Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ 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] long range restrain
Dear Colleagues, I am using gromacs 4.0.5, when I applied some long-ranged restrains (using NMR restrain tools), it stopped with output: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) However when I use mdrun -pd, it crashed. DO we have some ways to go around it? My molecule is quite big, so the restrain distance is larger than the cut-off. Regards Yuguang ___ 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] the temperature effect in the simulation
Do you have water ? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 The coupling constant sounds a bit small. The dynamics of fast motions may be affected more than you want, but I'm not a specialist of DNA and I don't know if it's a problem in that particular case. ref_t= 300 This indicates that your target temperature is 300K not 0K ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 It will also disassociate .It is strange. Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] settle issue
Thanks David, To switch on Dispersion Correction to the pressure will work ! Regards Yuguang Assist. Prof. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapore Tel: +65-63162885 email:ygmuATntu.edu.sg http://www.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, July 29, 2008 2:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] settle issue Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] hybrid or Hamiltonian REMD in gromacs
Dear David, Recently we have developed hybrid or Hamiltonian REMD method by modifying gromacs source code. If interested see our two JCP papers. If you, developers of GROMACS, are interested in including such method in new version of gromacs release. I am very pleased to share the idea here: In REMD module we let gromacs to load other programs, such as tinker or Delphi to calculate the energies. These energies, instead of total energies of the system, are input to REMD to calculate the exchange probabilities. URL: http://link.aip.org/link/?JCP/127/084119 URL: http://link.aip.org/link/?JCP/128/175105 Regards Yuguang Assist. Prof. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapore Tel: +65-63162885 email:ygmuATntu.edu.sg http://www.sbs.ntu.edu.sg/Staff/YGMu/index.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Talk slides from the Gromacs Stanford 2008 workshop
Sorry Eric, I cannot see anything. Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] regarding .gro file
In the last line. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ananya Debnath Sent: Friday, November 23, 2007 9:18 PM To: gmx-users@gromacs.org Subject: [gmx-users] regarding .gro file Hi, Can anyone tell me whether gromacs writes coordinate in .gro file with periodic boundary condition? Thanks, Ananya. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] REMD As A Function of Distance Between 2 Chains
Dear Huey Ling, In principle it is applicable. Then such REMD can be termed as Hamiltonian REMD instead of canonical temperature REMD. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huey Ling Tan Sent: Tuesday, November 13, 2007 2:24 AM To: Discussion list for GROMACS users Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] charge density of lipid
No, net charge density estimated from experimental data. Best regards Yuguang -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, September 01, 2007 4:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] charge density of lipid Mu Yuguang (Dr) wrote: Dear all, How to estimate the charge density of a lipid , the reason we want to do is that we try a model system to mimic the lipid environment. It seems out of GROMACS discussion range, but I believe many Gromacs users do lipid simulations. do you mean electron density? In that case there are plenty of tools in the CCP4 suite of programs. Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] charge density of lipid
I found one see this paper http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302891blobtype=p df it is defined by sigma_M Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, September 01, 2007 4:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] charge density of lipid Mu Yuguang (Dr) wrote: No, net charge density estimated from experimental data. what does it mean, how is it measured? you can have nuclear charge minus electron density, but this is not very accurate. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: more tahn
Dear all, When I use distance constrains(NMR), there happens such errors: Fatal error: More than 8 graph edges per atom (atom 1) I have more than 8 constrains on atom 1. What's reason? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Replica Exchange MD ... Exchange rates
That's great. Usually is 30%, of course also depends on how often you let exchange. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Carsten Baldauf Sent: Tuesday, July 10, 2007 5:43 PM To: Discussion list for GROMACS users Subject: [gmx-users] Replica Exchange MD ... Exchange rates dear gromacs-users// what would you think are good exchange rates between the replicas in a REMD? something like this? Replica exchange statistics Repl 499 attempts, 250 odd, 249 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .48 .53 .55 .54 .56 .53 .57 .55 .58 .57 .60 .63 .61 .60 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 101 133 131 136 137 142 125 147 142 137 141 151 168 152 153 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .53 .52 .55 .55 .57 .50 .59 .57 .55 .56 .61 .67 .61 .61 or lower? thanks in advance// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] PBC problem
Hi Tsjerk,
Thanks. I will try that.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 4:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Gromacs should automatically fix the box to meet the requirements
during an mdrun with pressure coupling (but does sometimes fail).
There is also a certain tolerance in gromacs for the deviations.
Anyway.., you can download a version of GMX3.2.1 from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.2.1-rtc.tgz
in which I modified editconf.c (and pbc.c/pbc.h) to have an option for
changing any triclinic box into a box which conforms to the gromacs
rules. Maybe you just want to get the parts of the code involved and
transfer them to GMX3.3.1, which should be quite straightforward. The
developers are welcome to incorporate the option/code if they like to
include it. The editconf option I added is -fix. Note that editconf
will still issue a warning about the skewness of the box, but on a
'fixed' structure, that should not occur anymore.
Hope it helps,
Tsjerk
On 5/16/07, Mu Yuguang (Dr) [EMAIL PROTECTED] wrote:
Thanks Tsjerk,
Probably because we use pressure coupling and the box size is
deformed.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dodecahedron.
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1
1
This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] PBC problem
Hi all,
We found some problems in using g_dist or g_minidist to calculate distance in
some PBC condition, dodecahedron
The output is as followed:
Back Off! I just backed up mindist.xvg to ./#mindist.xvg.2#
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
Can not fix pbc.
The input pdb is like this
REMARKGENERATED BY TRJCONV
TITLE Protein in water t= 394.3
REMARKTHIS IS A SIMULATION BOX
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1
MODEL0
ATOM201 C1' RA 7 13.130 -2.870 23.080 1.00 0.00
ATOM553 O4' RU18 44.730 54.920 28.830 1.00 0.00
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Milan Melichercik
Sent: Wednesday, August 23, 2006 7:50 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein in bilayer
Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal:
dear itamar
where is adress make-hole site?
thanks
3rd record on following page
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/
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RE: [gmx-users] PBC problem
Thanks Tsjerk,
Probably because we use pressure coupling and the box size is deformed.
Best regards
Yuguang
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dodecahedron.
CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1
This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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RE: [gmx-users] modify C6 directly in FF using sigma and epsilon
Dear David, In fact I really did as you said. First prepare a top file which explicitly include all bonded and nonbonded terms according to combination rule. In this way that top file can be called stand-alone top file (all the necessary parameters all included). Then you can do what you want. In my case I modify 1,4 interaction. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Mobley Sent: Friday, April 06, 2007 2:20 AM To: Discussion list for GROMACS users Subject: [gmx-users] modify C6 directly in FF using sigma and epsilon Gromacs users, I'm using a force field (the port of AMBER to GROMACS) which uses combination rules (combination rule 2), etc. in terms of sigma and epsilon. However, I need to be able to modify C6 directly (in particular, I want to be able to set it to zero). Can anyone give me any pointers on a relatively straightforward way to do that? I want to be able to continue using combination rule 2 but be able to separately modify C6 for a couple atom types (or interacting atom pairs). Obviously, one way I could work around this would be to explicitly specify all of the nonbonded interaction pairs in my topology so that the combination rules aren't used, then I could change the combination rule so that I could modify C6 and C12. But since that would be a real pain I'm hoping someone here can suggest something easier. Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] modify C6 directly in FF using sigma and epsilon
Yes. I did this way. I wrote it in small awk script. If you like I can share with it. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Friday, April 06, 2007 4:11 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] modify C6 directly in FF using sigma and epsilon David Mobley wrote: David, I'm using 3.3/3.3.1. Is there an easy tweak to the source code that would allow something like this? i.e. could I somehow easily tweak the bit where it reads the nonbond_params section so I can use an alternate combination rule there by specifying, say, a different nonbonded parameter type? It doesn't look like it. The sigma and epsilon are first read in the atomtypes section, and a matrix is filled in with sigma and epsilon. Then, if you overwrite a pair in the nonbond_types section two (because f symmetry) matrix elements are replaced. Finally, just before writing the file the values are converted to C6 and C12. It seems that your best bet is to write that little Perl script to convert the whole force field to C6/C12. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Can you help me ?
It seems the ions type not set. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, April 06, 2007 10:15 AM To: gmx-users@gromacs.org Subject: [gmx-users] Can you help me ? when I use the following command ,there always a error message.Can you help me ? Thank you very much ! command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr error message: . . creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4145 Cleaning up temporary file gromppD2IkOr --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Cl --- enviroment: ++ extra information: OS: Red Hat Linux AS4 fftw: fftw-3.1.2.tar.tar gromacs: gromacs-3.3.tar.gz installation : 1.fftw ./configure --enable-float make make install 2. gromacs ./configureCPPFLAGS=-I/gromacs/gromacs-3.3/include LDFLAGS=-L/gromacs/fftw-3.1.2/libbench2 make make install ++ *用搜狗拼音写邮件，体验更流畅的中文输入 http://goto.mail.sohu.com/goto.php3?code=mailadt-ta ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error when adding a unnatural amio acid
Please check the xlateat.dat file in share/top/ There is one line in it protein HT1H1 which will automatically change your atom name HT1 to H1. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yang Ye Sent: Wednesday, January 03, 2007 9:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Error when adding a unnatural amio acid You may try add residue name ASO to the end of /top/aminoacids.dat and also increment the number on the top. Regards, Yang Ye On 1/3/2007 8:55 AM, yuemin liu wrote: Hi, Everyone, I got Error when adding a unnatural amio acid in a protein. I have all the rtp and hdb file modified using information either from ffgmx.rtp ffgmx.hdb or thr rtp file form progdrg. There is no H1 in either rtp file or my new pdb file. When I try use pdb2gmx to generate top file, it always give the error message following; Atom H1 not found in rtp database in residue ASO, it looks a bit like H. I know it refers to the Hydrogen of the peptide bond which has nothing wrong there. Hope can get help from you with this, Thanks, __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a small bug?
Hi all We find that in mdp file, if it is written in this way: ewald_rtol = 1e-5 in fact it is the default value. But grompp cannot recognize it, finally in log file output it will appear: ewald_rtol = 0 And the simulation box will explode. But if it is written in this way: ewald_rtol = 0.1 everything is fine. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] a small bug?
Yes, you are right. It's a typo: l instead of 1. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, December 21, 2006 11:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] a small bug? Mu Yuguang (Dr) wrote: Hi all We find that in mdp file, if it is written in this way: ewald_rtol = 1e-5 in fact it is the default value. But grompp cannot recognize it, finally in log file output it will appear: ewald_rtol = 0 And the simulation box will explode. But if it is written in this way: ewald_rtol = 0.1 everything is fine. Nah... ewald_rtol = 1e-5 works fine. Check for typos, line-ending glitches, etc. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.
That's why I use a second step to modify the created top file to add such specific dihedral angle explicitly in the top file. I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, the periodic parameters of dihedral angles have been converted into Ryckaert-Bellemans ones. I have tried to find more info about this in the CHARMM and Gromacs documentations but I have not found much. Why exactly this conversion should be done since the periodic potential is implemented in both force fields? My problem is that several dihedral angles cannot be easily converted in RB parameters since their multiplicities is equal to 6 and the RB potential implemetation is limited to 5 constants. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] free energy: annihilation
Hi David, Recently I repeated some free energy solvation calculations according to the tutorial by David Mobly. I agree with him that when you do DMSO which has some high partial charges, You should do calculations with Coulomb and VdW separately. Otherwise unphysical results appear. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Mobley Sent: Saturday, August 26, 2006 9:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy: annihilation David, I'm trying to annihilate a complete DMSO box at constant volume. The dG/dlam values converge nicely but when I integrate the curve I get a Helmholtz energy that is almost exactly a factor of two different from the experimental value. Maybe this is too basic, but are you doing the transformation in vacuum also and subtracting? I assume you are trying to compute something like a hydration free energy, which means you have to complete a thermodynamic cycle that takes you from the full molecule in water to the full molecule in vacuum. I don't know any way to do this in GROMACS currently without also doing a separate vacuum calculation, because of the intramolecular interactions. Am I forgetting something here? Should I treat the intramolecular degrees of freedom in a special manner? You can, but you don't have to. One thing that can sometimes help convergence is to only turn off the intermolecular LJ interactions, which you can do by modifying the pairs list and explicitly stating appropriate LJ parameters, or (presumably) by using the new pairs types that Berk implemented, although I still haven't tested these myself. Currently I am only turning off the LJ and Coulomb terms. Should I turn off the angles and dihedrals as well? No, you don't want to do that. The other thing that can make some difference is your protocol. In particular: (1) Are you turning off the LJ and Coulomb terms simultaneously? I've always found that it is a lot harder to converge this calculation and get reliable answers than if you do the Coulomb interactions first and then do the LJ interactions. (2) What soft core parameters are you using for the LJ interactions? Some work much better than others. (My free energy tutorial has some information about doing the LJ transformation. If you want to do something really basic, you could try reproducing my value for methane: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial . I also list the soft core parameters that are optimal there.) (3) Make sure your PME parameters are good enough; sometimes free energy calculations can be pretty sensitive to this sort of thing (4) How curved is your dV/dlambda plot? TI can end up making a nontrivial amount of integration error, especially if you have nearly equal positive and negative areas under the curve (in which case the integration error could be on the same order of magnitude as the total integral). David David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: Θέμα: Re: [gmx-users] cyclic peptides
If I am not wrong, what you want to do is to build a topological file correctly for a cyclic peptide. You can do this: For example, your peptide has 5 (n=5) aa: CAAAD, You can build easily a linear topology file for a six (n+1) aa peptide chain ( with -ter switch answered by none): CAAADC, the last one should be the same as the first one. Then you can change the atom number for the last AA to the number for the first aa by just substracting the total number for the 5 AA from the atom number larger than that. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, August 17, 2006 10:51 PM To: Discussion list for GROMACS users Subject: Re: Θέμα: Re: [gmx-users] cyclic peptides Efi Mantzourani wrote: Hi David, had a look for the specbond entry, but apparently it is for creating a bond between ligand and receptor. I don't have that. Mine is not a special bond. it is just that pdb2gmx tries to find a terminus for all the chains. just try it anyway. you may have to sepcify the specific residue type of the N-terminus and C-terminus. */David van der Spoel [EMAIL PROTECTED]/* έγραψε: Efi Mantzourani wrote: Hi all, I am trying to run a gromacs trajectory on a ligand-receptor complex, where the ligand is a head-to-tail cyclic peptide. I add the -ter option in the pdb2gmx command, so that i can turn off the charged termini in the peptide. Unfortunately, it will only work keeping the N terminus as -NH2 (meaning it will add two hydrogens on the resulting structure) or as N (in this case it doesn't add any hydrogens). They are both wrong, as I want one hydrogen, like in a normal peptide bond. If i try to change the resulting files manually its a pain! The gro file is easy enough, but the topology file has to be altered so that the added hydrogen is in the correct atom and residue serial number. That means i have to change all the remaining atoms, all angles, dihedrals etc. Its just impossible as my complex has about 3.000 atoms! Any suggestions??? try making a specbond entry, you have to make sure that the coordinates are OK. please report back if succesfull. Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof.,
RE: [gmx-users] output energies by group
HI David, in the flying I means I want to output the total potential energy only for protein part ( total system is protein + solvent) when simulating is going on. I want to use that energy for some purpose. I know when using PME is not easy to get the energy group-decomposition, But when I use cut-off, there should be a way to do that, is it? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, August 05, 2006 3:40 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] output energies by group Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. What do you mean in the flying? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] output energies by group
Dear all, How to output energies of different groups during the MD simulation? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] diheadral PCA method
Dear All, Some of you want comments on the dihedral PCA analysis. Here I give the link to one comment on that which will appear in Proteins although we do not agree with their main result. Also you can find our reply to that comment. http://www.ntu.edu.sg/home/ygmu Best regards Yuguang Dr. Yuguang Mu Assistant Professor Division of Structural and Computational Biology School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: 63162885 Fax: 67913856 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
