Re: [gmx-users] --enable-threads fails.
Hi, The prefetching hardware is pretty good at hiding latencies, but obviously you'll get better performance when everything fits in cache. However, the largest data structures by far are the neighborlists, and their _total_ size for the simulation is independent of whether you are using multiple processes or multithreading. Cheers, Erik On Apr 10, 2007, at 10:46 PM, vipin sachdeva wrote: Thanks. Do you see L2 cache overflowing effects by putting multiple MPI processes on the same chip with the recent multi-core processors (Intel Woodcrest for instance)? Regards vipin On Tue, 10 Apr 2007, Erik Lindahl wrote: Hi, On Apr 10, 2007, at 10:15 PM, vipin sachdeva wrote: This thread on Feb 8 2006 mentions that threads are not yet functional. http://www.gromacs.org/pipermail/gmx-users/2006-February/019760.html Is the threads still not functional considering I still get the same error ? We are only using threads for experimental development of the nonbonded interaction loop. The multi-level-cache-locality features on modern CPUs (even NUMA on Opterons) means that you normally get better performance by partitioning the problem into separate MPI processes, where each process resides on a separate core. Cheers, Erik ___ 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 thewww 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 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] BHIS for HIS?
Hi, pdb2gmx tries to choose the HIS protonation based on hydrogen bond patterns in the structure, so unless you are absolutely certain you need the alternative state you should need to do anything. In the latter case, just edit the name in the PDB file (to HISB or HISH) prior to running pdb2gmx. Cheers, Erik On Apr 11, 2007, at 6:39 AM, Tsjerk Wassenaar wrote: Hi Rongliang Wu, You could try to get your hands on a GROMOS manual... Alternatively, draw the histidines using the information in the rtp files. Alternatively, take a histidine, run it through pdb2gmx with -his and try all options. Histidine has different protonation states, and one of the histidines is the one bound to heme iron. Cheers, Tsjerk On 4/11/07, Rongliang Wu [EMAIL PROTECTED] wrote: hello,gmx-users， i am trying to simulate a peptide with residue HIS, the default in pdb2gmx used HISB for HIS in both oplsaa and gromos96 force field, but i found there are HIS1,HISH,HISB etc in the rtp files, i am not sure whether HISB will suffice for my system, i intend to simulate the binding of surfactants with the peptide. what are the difference? is there anywhere i can find the detailed description for these residues? Rongliang Wu [EMAIL PROTECTED] 2007-04-11 ___ 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 -- 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 ___ 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] total simulation time for proteins in general
Hi, On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote: 2. Is minimisation in GROMACS only used as a precursor to the md- simulation to remove bad contacts, or can we also use it effectively to minimize a raw modelled ab-initio structure.? Well, technically you can of course use it, but any energy minimization algorithm will only take you to a close local minimum in the energy (=enthalpy) landscape. If you want your model to get closer to the native state you need refinement, and that's way more complicated. Search the literature for techniques like simulated annealing, Replica-exchange molecular dynamics, etc. Cheers, Erik ___ 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] question about the total-energy of energy minimization
Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 - 919.923 Coulomb-(SR) -35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.120524.520248.7-341.91 - 11614.9 Kinetic-En. 0 0 0 0 0 Total-Energy 0 0 0 0 0 Temperature 0 0 0 0 0 Why the Total-energy is not the sum of Potential and Kinetic-En.? Thanks! ___ 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] energy minimization error
hello,everyone I am new of gromacs. I am running a sample following the Tutorial for Drug - Enzyme Complex,which was written by John E.Kerrigan,Ph.D. When I run the energy minimization ,it has error as followed. Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 11500 ] Please report this to the mailing list (gmx-users@gromacs.org) I don't know Why it has such error? What should I do? Can you help me? ___ 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] energy minimization error
Check your trajectory to visually check whether it has exploded. This may lead you to check all your input files, especially the mdp files. This error may happen even in good settings, but Variable ci shall not differ much from the desired range. In that case, I will turn Pressure coupling off nd restart the simulation from an earlier time. On 4/11/2007 5:13 PM, ?? wrote: hello,everyone I am new of gromacs. I am running a sample following the Tutorial for Drug - Enzyme Complex,which was written by John E.Kerrigan,Ph.D. When I run the energy minimization ,it has error as followed. Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 11500 ] Please report this to the mailing list (gmx-users@gromacs.org) I don't know Why it has such error? What should I do? Can you help me? ___ 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] overcome the integration problem (installing CVS)
Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Best, Itamar --- Prediction is very difficult, especially about the future - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://www.uq.edu.au/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ 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] overcome the integration problem (installing CVS)
On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar --- Prediction is very difficult, especially about the future - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://www.uq.edu.au/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ 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] overcome the integration problem (installing CVS)
Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar The stable version does not have the fix (because it will change results). -- 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
Re: [gmx-users] question about the total-energy of energy minimization
Qiao Baofu wrote: Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 -919.923 Coulomb-(SR) - 35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.120524.520248.7-341.91 -11614.9 Kinetic-En. 0 0 0 0 0 Total-Energy 0 0 0 0 0 Temperature 0 0 0 0 0 Why the Total-energy is not the sum of Potential and Kinetic-En.? Thanks! In a minimization, you have no kinetic energy. Thus the potential energy is the total energy and nobody bothered copying over the value. Mark ___ 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] Hi all
Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? If so how can I incoroprate this into gromacs? and also How to get the starting configuration for the poysiloxanes? ( like .gro, .top, .itp files) Thanking you in advance ann ___ 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] overcome the integration problem (installing CVS)
From: David van der Spoel [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] overcome the integration problem (installing CVS) Date: Wed, 11 Apr 2007 12:13:13 +0200 Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar The stable version does not have the fix (because it will change results). -- David. I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] Hi all
ann rose wrote: Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? Yes - this information is part of the force field. If so how can I incoroprate this into gromacs? You will need a thorough working knowledge of at least chapter 5 of the manual, and plenty from earlier sections. This will also let you assess whether the range of functions computed by gromacs is suitable for your forcefield. and also How to get the starting configuration for the poysiloxanes? ( like .gro, .top, .itp files) .gro files are structure files... you're responsible for generating them. Search the mailing list for suggestions. .top files can be generated by pdb2gmx if you can generate suitable .rtp monomers, but life may be messy here for branched polymers... you may need to make these by hand. .itp files are included by .top files and include your basic force field files as well as regularly recycled units like solvents... you need to make these. Mark ___ 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] Prot_prep_problem
Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output file from stage 1 using the -inter flag to get my final .top .gro and .pdb files I find that at the end of step 1 the pdb output is stripped of hydrogens. In the second stage I find that the .top file has the hydrogens listed (only polar hydrogens) but the pdb output is still without any hydrogens. I want to follow the gromacs tutorial titled GROMACS Tutorial for Drug Enzyme Complex. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf here they have used a prepared protein pdb file while merging the ligand coordinates to form the final complex. My questions are 1) why the pdb file written in step two does not contain the hydrogens and how can i solve this issue? 2) Is there any other way to prepare the ligand-protein complex without using the protein .pdb output? 3) This is a slightly unrelated question. Could some body guide me to any tutorials etc where they have shown how to calculate gausssian charges for the ligand and then incorporate into the gromacs ligand file? I can provide the protein structure file. I couldnt load it to the group mail because of size limitations Thanking you in anticipation Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ 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] Prot_prep_problem
HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final trr in order to analyze for instance the violated NOE. Skip last question, sorry :) Regards andrea pkmukher wrote: Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output file from stage 1 using the -inter flag to get my final .top .gro and .pdb files I find that at the end of step 1 the pdb output is stripped of hydrogens. In the second stage I find that the .top file has the hydrogens listed (only polar hydrogens) but the pdb output is still without any hydrogens. I want to follow the gromacs tutorial titled GROMACS Tutorial for Drug – Enzyme Complex. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf here they have used a prepared protein pdb file while merging the ligand coordinates to form the final complex. My questions are 1) why the pdb file written in step two does not contain the hydrogens and how can i solve this issue? 2) Is there any other way to prepare the ligand-protein complex without using the protein .pdb output? 3) This is a slightly unrelated question. Could some body guide me to any tutorials etc where they have shown how to calculate gausssian charges for the ligand and then incorporate into the gromacs ligand file? I can provide the protein structure file. I couldnt load it to the group mail because of size limitations Thanking you in anticipation Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ 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 -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ 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] Prot_prep_problem
I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final trr in order to analyze for instance the violated NOE. Skip last question, sorry :) Regards andrea pkmukher wrote: Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output file from stage 1 using the -inter flag to get my final .top .gro and .pdb files I find that at the end of step 1 the pdb output is stripped of hydrogens. In the second stage I find that the .top file has the hydrogens listed (only polar hydrogens) but the pdb output is still without any hydrogens. I want to follow the gromacs tutorial titled GROMACS Tutorial for Drug – Enzyme Complex. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf here they have used a prepared protein pdb file while merging the ligand coordinates to form the final complex. My questions are 1) why the pdb file written in step two does not contain the hydrogens and how can i solve this issue? 2) Is there any other way to prepare the ligand-protein complex without using the protein .pdb output? 3) This is a slightly unrelated question. Could some body guide me to any tutorials etc where they have shown how to calculate gausssian charges for the ligand and then incorporate into the gromacs ligand file? I can provide the protein structure file. I couldnt load it to the group mail because of size limitations Thanking you in anticipation Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ 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 -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ 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] Prot_prep_query
/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ 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 -- Message: 2 Date: Wed, 11 Apr 2007 12:13:13 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] overcome the integration problem (installing CVS) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Stable version: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx HEAD Branch cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Best, Itamar The stable version does not have the fix (because it will change results). -- 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 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ++ ++ -- Message: 3 Date: Wed, 11 Apr 2007 21:14:55 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] question about the total-energy of energy minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Qiao Baofu wrote: Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08-919.923 Coulomb-(SR) - 35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.1 20524.520248.7-341.91-11614.9 Kinetic-En. 0 0 0 0 0 Total-Energy 0 0 0 0 0 Temperature 0 0 0 0 0 Why the Total-energy is not the sum of Potential and Kinetic-En.? Thanks! In a minimization, you have no kinetic energy. Thus the potential energy is the total energy and nobody bothered copying over the value. Mark -- Message: 4 Date: Wed, 11 Apr 2007 13:39:45 +0200 From: ann rose [EMAIL PROTECTED] Subject: [gmx-users] Hi all To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] om Content-Type: text/plain; charset=iso-8859-1 Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? If so how can I incoroprate this into gromacs? and also How to get the starting configuration for the poysiloxanes? ( like .gro, ..top, .itp files) top, .itp files) Thanking you in advance ann -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070411/05362ed7/attachment-0001.html -- Message: 5 Date: Wed, 11 Apr 2007 13:40:50 +0200 From: Berk Hess [EMAIL PROTECTED] Subject: Re: [gmx-users] overcome the integration problem (installing CVS) To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; format=flowed From: David van der Spoel [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users
Re: [gmx-users] overcome the integration problem (installing CVS)
Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on NVE dynamics, they must be affected similarly. For example, for Nose-Hoover thermostats, there exists a conserved quantity. I would expect that this fix would also improve that conserved quantity, wouldn't it? One feature that would be useful is that for any algorithm that has a conserved energy-like quantity, there should be an entry in the .edr file with that quantity. It would be a useful check for algorithmic consistency. I don't think this is yet in GROMACS, though I could be wrong -- I haven't examined the CVS that recently. Best, Michael Shirts Research Fellow Department of Chemistry Columbia University ___ 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] overcome the integration problem (installing CVS)
Michael Shirts wrote: Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on NVE dynamics, they must be affected similarly. For example, for Nose-Hoover thermostats, there exists a conserved quantity. I would expect that this fix would also improve that conserved quantity, wouldn't it? One feature that would be useful is that for any algorithm that has a conserved energy-like quantity, there should be an entry in the .edr file with that quantity. It would be a useful check for algorithmic consistency. I don't think this is yet in GROMACS, though I could be wrong -- I haven't examined the CVS that recently. How about total energy? In tends to be constant in NVE simulations. I don't know what the conserved property would be in an NVT simulation. -- 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] Re:overcome the integration problem (installing CVS)
How about total energy? In tends to be constant in NVE simulations. I don't know what the conserved property would be in an NVT simulation. David. For most algorithms that give correct ensembles, there are pseudo-energy properties that are conserved. For NVE, it's obviously the energy. For Nose-Hoover NPT, there's a term involving the mass of the coupling to the heat reservoir that, when added to the scaled energy term produces a quantity that will be conserved. For Parrinello-Rahman dynamics, there's a similar term involving the coupling to the pressure bath. It would. Although I would still argue that when using a thermostat there is in most cases no useful quantity that would be affected by the current, very small, velocity inaccuracies. Berk I think algorithmic self-consistency could generally be justified as useful. If one is applying a certain algorithm, it's good to have a measure of how well that algorithm is being implemented, so one can be sure that any errors are negligible. I agree with Berk that such inaccuracies are small. But it's good to have a measure of how small they are built in, just to be sure! :) Best, Michael ___ 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] wall_atomtype
Greetings to All
I have a question about a new feature in the cvs code
and I was wondering if there was anybody who could
give
me a hand of a bit of help.
Thanks in advanced.
I am working on a project that involves simulation of
confined water between two hydrophobic surfaces.
I noticed that recently there was an addition to the
gromacs source code that would allow for this kind of
simulations
I downloaded the cvs source code to try out this new
feature, ran a small simulation of water with pbc=xy
and no surfaces and could see the water evaporate as
was expected
The problems occurs when I need to add surfaces to the
simulation. There are some new variables that I don't
know how to set and I have not been able to figure
this out from the source code.
What are the appropriate values for wall_atomtype?
I want to have a LJ interaction between the wall and
the oxygen atom in
the water molecule.
How can I do this with this new feature?
In the function do_walls we have (file wall.c)
if (ir-wall_type == ewt93) {
fac_d[w] = ir-wall_density[w]*M_PI/6;
fac_r[w] = ir-wall_density[w]*M_PI/45;
} else if (ir-wall_type == ewt104) {
fac_d[w] = ir-wall_density[w]*M_PI/2;
fac_r[w] = ir-wall_density[w]*M_PI/5;
}
Where are these factor coming from, is there a
reference that I can look at?
What would be appropriate values for the variable
wall_density?
Would these be the appropriate changes to my
grompp.mpd file to get
this feature working of is there anything else that I
need to add?
pbc=xy
nwall=2
wall_type=9-3
wall_atomtype = ? ?
wall_density = ? ?
I apologized if these are too many questions!!
I realized this a very new feature and probably it is
not well tested, yet I would like to try it out and
see if I can use this for my project
Any help would be really appreciated.
Thanks a lot.
Kind regards,
Manuel Valera
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[gmx-users] Prot_prep_query
Hi, Thanks for your suggestions. I was using the 0 option gromos FF in pdb2gmx. As you said the behavior is strange. However i found a fix. I was using a 2 step procedure 1) strip hydrogen output pdb 2) input pdb write output pdb with -inter flag instead i used 1) strip hydrogen output pdb 2) input pdb write pdb gro top using -inter flag (gro has hydrogens, pdb does not) 3) use gro as input take pdb output (pdb has hydrogens) Thanks Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ 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
