Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ 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
[gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? No. If your lipids are just a 'solvent', then treat them as you would treat water. If you are specifically interested in the lipid conformations and dynamics then treat them as you would treat water if you were interested in the specific solvation and dynamic properties of water. Lipid bilayers are essentially a bulk system, the same as water, but different from an embedded protein. Personally, I do 5 ns posre on the protein after insertion and then it takes 15+ ns for general protein equilibration. This is from the make-hole version of gmx 3.1.4, which I consider to be optimal for reducing equilibration time, so your required equilibration time may be greater... check time-dependent RMSDs. On a slightly separate note, I know that many papers do not give a full methods description, but many also do. If you have indeed read many membrane protein simulation papers and it is your intention to question if it is an absolute truth that lipids need not be position restrained during equilibration then that is something that you would need to elucidate yourself as I have not seen that studied explicitly (although I highly doubt that this is the case). Chris. ___ 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: still system exploid
Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. You can decrease timestep even more for some time and when system relax properly return it to the initial value. You can exclude some kind of interactions in your system. You have plenty of things to do... If nothing still helps, send me all your system with all input files and forcefield - everything you use to run - and I will try to help you once having time. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] Change of force field: ffgmx ff53a5
Dear all, i have changed the topologie but i have a question regarding the following simulations. With ffgmx the length of the cut-offs (/rcoulomb /and /rvdw/) is standard 1.0 (default adjustment by GROMACS). I believe that i've seen some time ago that for the GROMOS96 force fields the cut-offs should be larger (think it was 1.3 or so?!?), but i do not find it again. So i want to ask if my memorys are correct and what the values are be. Thanks for an answer. Thomas ___ 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] T-WHAM for replica
Hello everyone, Does anyone have a script to do T-WHAM analysis of replica exchange trajectories? Any help would be great! Thanks, Andrea ___ 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] Change of force field: ffgmx ff53a5
On Wed, 17 Sep 2008 11:56:41 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: Dear all, i have changed the topologie but i have a question regarding the following simulations. With ffgmx the length of the cut-offs (/rcoulomb /and /rvdw/) is standard 1.0 (default adjustment by GROMACS). I believe that i've seen some time ago that for the GROMOS96 force fields the cut-offs should be larger (think it was 1.3 or so?!?), but i do not find it again. So i want to ask if my memorys are correct and what the values are be. The non-bonded interactions in GROMOS force fields are parameterized with a twin-range cutoff 0.8/1.4 nm and reaction-field to compensate for the long-range (after 1.4 nm) electrostatics. Thanks for an answer. Thomas ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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] PBS Script - trjconv Options
VENKATESH HARIHARAN wrote: Hello, Simple question. I am running constraint pulling and getting the .xtc and .tpr output files in order to create a pdb video using trjconv. I am running simulations on a cluster, and so a pbs script must be submitted with the necessary commands. When using trjconv command, the group must subsequently be specified. Is there any way to modify the below command to also select a specific group (i.e. - 1 for 'Protein'). For example, when using mdrun, the -ff option can be used to specify which forcefield to use. Is there something similar to this with regards to the group selection when using trjconv? Thanks. Something like this? http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive -Justin trjconv -s peptide.tpr -f trajectory.xtc -o pullvideo.pdb __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] restarting REMD checkpoint gmx-cvs
Hi users, I would like to restart some REMD simulations done with the cvs code with the new checkpoint feature, but I'm unsure if I'm doing it right. Each replica has its own state#.cpt file, but it seems to me that the -cpi option of the cvs mdrun (at version 3.3.99_development_20080718) only allows one checkpoint file. Is that enough for a correct restart? I did some tests, and it does restart the dynamics, however I'm not sure if it's done ok. Why then, do we get a checkpoint file for each replica? Best, Guillem ___ 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: Re: [gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ 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
[gmx-users] Re: Change of force field: ffgmx ff53a5
Ok, then i would take to following parameters: _x is vdw or coulomb rlist 1.7 (must be greater then r_x) r_x1.4 r_x_switch0.8 x_typeshift right?!? Thomas ___ 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] Re: Change of force field: ffgmx ff53a5
On Wed, 17 Sep 2008 14:27:57 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: Ok, then i would take to following parameters: _x is vdw or coulomb rlist 1.7 (must be greater then r_x) r_x1.4 r_x_switch0.8 x_typeshift right?!? No, rlist 0.8 nstlist 5 rcoulomb 1.4 rvdw 1.4 vdwtype cutoff coulombtype Reaction-field Thomas ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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: Change of force field: ffgmx ff53a5
Thank you. But i have one last question: For epsilon_rf i use the relative permittivity of the medium. I simulate in vacuum so epsilon_rf would be 1? Thomas On Wed, 17 Sep 2008 14:27:57 +0200 Thomas Schlesier schlesi at uni-mainz.de http://www.gromacs.org/mailman/listinfo/gmx-users wrote: / Ok, then i would take to following parameters: // // _x is vdw or coulomb // // rlist 1.7 (must be greater then r_x) // r_x1.4 // r_x_switch0.8 // x_typeshift // // right?!? /No, rlist 0.8 nstlist 5 rcoulomb 1.4 rvdw 1.4 vdwtype cutoff coulombtype Reaction-field / Thomas // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // 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 gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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] Re: Change of force field: ffgmx ff53a5
On Wed, 17 Sep 2008 15:00:17 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: Thank you. But i have one last question: For epsilon_rf i use the relative permittivity of the medium. I simulate in vacuum so epsilon_rf would be 1? GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. Thomas On Wed, 17 Sep 2008 14:27:57 +0200 Thomas Schlesier schlesi at uni-mainz.de http://www.gromacs.org/mailman/listinfo/gmx-users wrote: / Ok, then i would take to following parameters: // // _x is vdw or coulomb // // rlist 1.7 (must be greater then r_x) // r_x1.4 // r_x_switch0.8 // x_typeshift // // right?!? /No, rlist 0.8 nstlist 5 rcoulomb 1.4 rvdw 1.4 vdwtype cutoff coulombtype Reaction-field / Thomas // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // 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 gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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] About QH entropy, could you please help me?
Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran. Li Yang wrote: Dear Ran Friedman I'm sorry to disturb you, my name is Li Yang, I'm a chinese student. I've read some paper about the calculation of QH entropy: (a)Jurgen Schlitter_ChemPhysLett1993_215_617, (b)Ioan Andricioaei_JChemPhys2001_115_6289(quasiharmonic approximation). There is still something confuse me. (1) Why the number of the eigenvalues is 3n-6 (the last 6 values are close to zero) but not 3n ? I practice some small examples by gromacs. (256 argon atoms in a box of 2.3nm^3, you can find this example in paper(b)). For g_covar, when -nofit, the number of eigenvalues is 3n; when -fit the number is 3n-6. It seems there are some freedoms constrainted in the fit process. The paper' conclusion is based on a assumption that hwkT, say, the high frequencies vibrate (both rotation and translations, right?) can be omitted for the entropy calculations, as it were, the contributions of them is too small to be omitted. Are the freedoms mentioned above represent the freedoms of rotations and translations of the molecules. I don't know. Maybe the answer is in those papers, but I cannot catch it. While how to use the nofit result and fit result? The eigenv.agr in the attachment includes fit and nofit results for the example: 256 argon atoms in a box of 2.3nm^3. Why there is a big difference between them? (2) I split some time-segment to obtain the entropies in each stage to get the convergence variation of the entropy. But I doubt the feasibility of this method. If wrong, how to do? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? I apologize in advance if I disturb you. Thank you very much. Waiting for you reply. Best Li Yang Li Yang [EMAIL PROTECTED] 2008-09-17 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ 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] sampling conformation on the basis of RMSD value
Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value say A nanometer. Can anybody suggest me a way to do the same ? I heard of g-cluster command for the same, but don't know how can I use it for given RMSD difference ? Can I do it before giving the final run command, so it will sample the conformation during the run on the basis of RMSD value ? With Thanks, Vivek ___ 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] simulation in vacuum
/ Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Thanks for an answer Thomas ___ 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] simulation in vacuum
On Wed, 17 Sep 2008 16:14:08 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: / Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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] About QH entropy, could you please help me?
(1) 6 eigenvalues represent rotation and translation. For (very) small molecules, these can be quite substantial, see Carlsson and Aqvist, /J. Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the rotation and translation. You can search the literature for papers that discuss the QH approximation as well. The motions are not really harmonic - this is why it's an approximation. I've received very similar results to Carlsson and Aqvist for benzene and palmatic acid with GMX. (2) The values you get depend on the sampling and the conversion of the simulations. To improve sampling, you have to store the coordinates frequently enough (so you get more samples). In addition, the simulation should be long enough to give you meaningful results - and both depend on the system which you study. Checking for convergence can be done by repeating the calculations on different time windows, as you suggested. (3) If you want to study the entropy, you have to sure it convergence. Otherwise, it depends on what you want to calculate. (4) Try to see if you really simulate the same system, and maybe try other systems like the ones in the above mentioned paper. There can be dozens of things that can change and since I didn't run these simulations I can't be of much help here. As for the units, I don't really remember what I used for frequencies, only that the final result should be in J/(mol K) or Cal/(mol K). By following the script, with the remarks, you should get the right units. Ran. Ran Friedman wrote: Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran. Li Yang wrote: Dear Ran Friedman I'm sorry to disturb you, my name is Li Yang, I'm a chinese student. I've read some paper about the calculation of QH entropy: (a)Jurgen Schlitter_ChemPhysLett1993_215_617, (b)Ioan Andricioaei_JChemPhys2001_115_6289(quasiharmonic approximation). There is still something confuse me. (1) Why the number of the eigenvalues is 3n-6 (the last 6 values are close to zero) but not 3n ? I practice some small examples by gromacs. (256 argon atoms in a box of 2.3nm^3, you can find this example in paper(b)). For g_covar, when -nofit, the number of eigenvalues is 3n; when -fit the number is 3n-6. It seems there are some freedoms constrainted in the fit process. The paper' conclusion is based on a assumption that hwkT, say, the high frequencies vibrate (both rotation and translations, right?) can be omitted for the entropy calculations, as it were, the contributions of them is too small to be omitted. Are the freedoms mentioned above represent the freedoms of rotations and translations of the molecules. I don't know. Maybe the answer is in those papers, but I cannot catch it. While how to use the nofit result and fit result? The eigenv.agr in the attachment includes fit and nofit results for the example: 256 argon atoms in a box of 2.3nm^3. Why there is a big difference between them? (2) I split some time-segment to obtain the entropies in each stage to get the convergence variation of the entropy. But I doubt the feasibility of this method. If wrong, how to do? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? I apologize in advance if I disturb you. Thank you very much. Waiting for you reply. Best Li Yang Li Yang [EMAIL PROTECTED] 2008-09-17 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman
[gmx-users] Re: [Fwd: still system exploid]
Good file. I see no problems in it. However I asked not only for the gro file but also force field parameters. If you really need help the best variant to provide all the system you try to simulate. I could not send my file by gmx user because of this I attached it to email. Thanks for your all helps. Morteza -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] g_dipoles index file
Hi, I am trying to calculate the N-H dipole autocorrelation function of my protein using g_dipoles. The mentioned the atom numbers of these two in my index file. I have given the following command: g_dipoles -f md_minim_traj.trr -s MD_1BA4.tpr -P 2 -corr mol -c dipo_corr.xvg -b -e 1000 -n NH.ndx The output is the following: Program g_dipoles, VERSION 3.3.1 Source code file: gmx_dipoles.c, line: 1014 Fatal error: index[1]=18 does not correspond to the first atom of a molecule Here the atom numbers I have defined in the index file are 18 and 19. What is the problem in defining the index file ? 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
Re: [gmx-users] simulation in vacuum
Xavier Periole wrote: On Wed, 17 Sep 2008 16:14:08 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: / Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. If I recall a previous discussion (somewhere in the archive), ffG43b1 is not actually a vacuum force field, but rather one where all of the titratable groups are in their neutral forms. As for whether or not that is applicable to a vacuum simulation, I guess you'll have to decide. -Justin In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] simulation in vacuum
/ Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ 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 I looked in some older papers but found no values for epsilon_r and _rf. From older posts of this mailing list I got the impression that epsilon_r = 1 and epsilon_rf the value of the relative permitivity of the medium. In the case of a simulation in vacuum epsilon_rf would be also 1 and then I have no correction from the reaction field, also grompp tells me that epsilon_r = epsilon_rf would be meaningless with a reaction field. So I'm puzzeld. If both epsilon values have the same value, is it then equal to normal cut-offs (type = cut-off)? Sorry for the many questions. Thomas ___ 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] sampling conformation on the basis of RMSD value
vivek sharma wrote: Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value say A nanometer. Can anybody suggest me a way to do the same ? I heard of g-cluster command for the same, but don't know how can I use it for given RMSD difference ? The logfile printed out by g_cluster gives clusters of structures based on their RMSD, with the constituent members printed out next to the cluster number. The cluster members are shown in terms of the timeframe corresponding to the frame. You can then extract any frames you wish using trjconv -dump. -Justin Can I do it before giving the final run command, so it will sample the conformation during the run on the basis of RMSD value ? With Thanks, Vivek ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] simulation in vacuum
Actually in vaccum the RF is meaningless ... use cutoff. On Wed, 17 Sep 2008 18:49:38 +0200 Thomas Schlesier [EMAIL PROTECTED] wrote: / Thank you.// But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper.So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ 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 I looked in some older papers but found no values for epsilon_r and _rf. From older posts of this mailing list I got the impression that epsilon_r = 1 and epsilon_rf the value of the relative permitivity of the medium. In the case of a simulation in vacuum epsilon_rf would be also 1 and then I have no correction from the reaction field, also grompp tells me that epsilon_r = epsilon_rf would be meaningless with a reaction field. So I'm puzzeld. If both epsilon values have the same value, is it then equal to normal cut-offs (type = cut-off)? Sorry for the many questions. Thomas - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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] simulation in vacuum
Thomas Schlesier wrote: / Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. AFAIK the only difference between vacuum force field and normal force field in GROMOS is the protonation state of the side-chains (please check that this is still correct in the current force fields). For vacuum simulations of relatively small proteins I would recommend using no cut-off at all. Since there is no direct experimental information about protein structure in vacuum, there is no reason to use the solution values of the cut-offs. Without the shielding of the water everything is different. Another interesting problem is to determine which residues to protonate in the gas phase, see e.g. Patriksson et al. Biochemistry 46 pp. 933-945 (2007) http://pubs.acs.org/cgi-bin/download.pl?bi061182y/B6CC. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php I looked in some older papers but found no values for epsilon_r and _rf. From older posts of this mailing list I got the impression that epsilon_r = 1 and epsilon_rf the value of the relative permitivity of the medium. In the case of a simulation in vacuum epsilon_rf would be also 1 and then I have no correction from the reaction field, also grompp tells me that epsilon_r = epsilon_rf would be meaningless with a reaction field. So I'm puzzeld. If both epsilon values have the same value, is it then equal to normal cut-offs (type = cut-off)? Sorry for the many questions. Thomas ___ 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., Professor of Biology 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] ligand parameterization for amber port in gmx
Dear people, I have parameterized a ligand with one phosphate and one pyrophospate group using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx conversion tool (http://www.alchemistry.org/wiki/index.php/Free_Energy_Tools) and then used in gromacs for energy minimization. The geometry looks fine after in vacuo EM and EM in water (ffamber tip3p model from amber ports) of the ligand alone (not bound to protein!). Minimizing the ligand in its binding mode as seen in the corresponding PDB (using the amber03 ff) also works fine if magnesium ions are NOT included. Including magnesium ions however leads to severe deformations of the phosphate and pyrophosphate groups. I suspect it has something to do with not including the magnesium ions in the parameterization. Can anybody please give me a hint on how to solve this problem? Thanks a lot, Merc ___ 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] still system exploid
Morteza Khabiri wrote: Dear gmxuser, Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. To reply the question that said what is your system? My system is ACETONE + water + protein which i mixed water and protein before and i just put the protein in the solution of ACETONE and water. Are you sure the water+acetone box in which you insert your protein is well equilibrated? In my case, I generally make a small box of solvent and run a MD simulation of 5-10 ns. Then I solvate my peptides with genbox and this small box. Finally, I minimize. When things go really wrong like in your case, I remove a thin layer of solvant (~0.3 nm) around my peptide, before minimization. I also increase the equilibration time in that later case. If you directly use a box the size of your protein, you probably have to remove manually overlapping solvent molecules before minimization. You may also try to minimize in 2 steps: 1) minimization of the solvent with restraints on the solute, 2) minimization of the whole system. Nicolas About mdp that has a popc, I should say that this mdp was fpr my membrane which i used it before and i just change some of the parameter of this file and because the name was not important i did not change it. I am sorry my gro file is big and because of this the gmxmail servic avoid to send it. I will send to privet email. for coulomb i use the followings: 1- coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 2- coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 again thanks Morteza ___ 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 begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:PhD tel;work:(403) 220-6869 tel;fax:(403) 289-9311 x-mozilla-html:TRUE version:2.1 end:vcard ___ 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] topology of cyclohexane
Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Vitaly ___ 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] simulation in vacuum
David is right! There are no FF that has been parametrized for vaccum simulations and the best you can do is using a classical FF and neutralize charges to avoid collapses ... be aware of what you do ... On Wed, 17 Sep 2008 19:13:33 +0200 David van der Spoel [EMAIL PROTECTED] wrote: Thomas Schlesier wrote: / Thank you. // But i have one last question: //For epsilon_rf i use the relative permittivity of the medium. I simulate in //vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1 instead of the other GROMOS96 force fields? That would be the right choice for the GROMOS43 ff series. AFAIK the only difference between vacuum force field and normal force field in GROMOS is the protonation state of the side-chains (please check that this is still correct in the current force fields). For vacuum simulations of relatively small proteins I would recommend using no cut-off at all. Since there is no direct experimental information about protein structure in vacuum, there is no reason to use the solution values of the cut-offs. Without the shielding of the water everything is different. Another interesting problem is to determine which residues to protonate in the gas phase, see e.g. Patriksson et al. Biochemistry 46 pp. 933-945 (2007) http://pubs.acs.org/cgi-bin/download.pl?bi061182y/B6CC. In the GROMACS manual i found that the cut-off-distance must at least be 1.4 nm for the GROMOS96 force field. Never believe what is written in a manual :)) It is always better to keep the values that are used for parameterization (the one I gave you) when using a force field. The idea that bigger = better does not work ... you change the balance of forces and thus the properties of the force field. So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7? (the problem is that the only reference i find for ffG43b1 is the GROMOS manual, and that's not free avaible) Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers) would describe the simulation setup: no need of the manual for this. Thanks for an answer Thomas ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php I looked in some older papers but found no values for epsilon_r and _rf. From older posts of this mailing list I got the impression that epsilon_r = 1 and epsilon_rf the value of the relative permitivity of the medium. In the case of a simulation in vacuum epsilon_rf would be also 1 and then I have no correction from the reaction field, also grompp tells me that epsilon_r = epsilon_rf would be meaningless with a reaction field. So I'm puzzeld. If both epsilon values have the same value, is it then equal to normal cut-offs (type = cut-off)? Sorry for the many questions. Thomas ___ 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., Professor of Biology 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - ___ 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
Re: [gmx-users] sampling conformation on the basis of RMSD value
Hi there,
below you can find a dirty perl script that I used to extract
structure from a trr by reading the cluster.log file from g_cluster
Just remove in the cluster.log file all the lines until the (included):
cl. | #st rmsd | middle rmsd | cluster members
# paste from here -
use warnings;
open(IN,$ARGV[0]) or die $!;
while($line=IN) {
chomp $line;
@tmp=split(/\|/,$line);
$clu=$tmp[0];
$strucs=$tmp[3];
$tmp1=$tmp[2];
@new=split(/ +/,$tmp1);
$middle=$new[1];
if ($clu =~ /\d/) {
$in=$clu;
$MIDDLE{$in}=$middle;
push @{ $hash{$clu} }, $strucs;
}
unless ($clu =~ /\d/) {
push @{ $hash{$in} }, $strucs;
}
}
foreach $key (keys %hash) {
foreach $ind (@{$hash{$key}}) {
@test=split(/ +/,$ind);
foreach $ele (@test) {
if($ele =~ /\S/) {
push @{ $nhash{$key}}, $ele;
}
}
}
}
foreach $k (keys %nhash) {
$size=scalar(@{$nhash{$k}});
foreach $l (@{$nhash{$k}}) {
#HERE you may have a system call
print $k - $l\n;
}
#print $k - $size\n;
}
foreach $key (keys %MIDDLE) {
# print $key - $MIDDLE{$key}\n;
}
#-- paste to here ---
perl extract.pl cluster.log
The line print $k - $l\n can be removed and there you may have a
system call to trjconv to dump all your structure from the trr.
Please let me know if it is not so much clear ...
andrea
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
- Original Message -
From: Justin A. Lemkul [EMAIL PROTECTED]
Date: Wednesday, September 17, 2008 6:42 pm
Subject: Re: [gmx-users] sampling conformation on the basis of RMSD value
vivek sharma wrote:
Hi There,
I have a 5 nsec trajectory file for my system...and a RMSD plot
for the
same.
while doing simulation I have sampled the frame at each 500 ps,
Now I want to choose conformation on the basis of RMSD values,
like
conformation which has RMSD difference of some value say A
nanometer. Can anybody suggest me a way to do the same ?
I heard of g-cluster command for the same, but don't know how can
I use
it for given RMSD difference ?
The logfile printed out by g_cluster gives clusters of structures
based on their
RMSD, with the constituent members printed out next to the cluster
number. The
cluster members are shown in terms of the timeframe corresponding
to the frame.
You can then extract any frames you wish using trjconv -dump.
-Justin
Can I do it before giving the final run command, so it will
sample the
conformation during the run on the basis of RMSD value ?
With Thanks,
Vivek
--
--
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--
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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begin:vcard
n:Spitaleri;Andrea
fn:Andrea Spitaleri
tel;fax:+390226434153
org:Dibit Scientific Insititute;BioMolecular Structure
adr:;;via Olgettina 58;Milan;;24132;Italy
version:2.1
email;internet:[EMAIL PROTECTED]
title:Dr
end:vcard
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[gmx-users] harmonic restraint
Dear all GROMACS users, I'm new in protein simulation. Does anybody let me know in what subroutine the harmonic restraint is implemented? If I would like to trace back to the subroutine from md.c, how can I do that? I really appreciate any comments on such a beginner's question. Best, Jae H. Park === Jae Hyun Park, Ph.D. Visiting Scholar 3215 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) [EMAIL PROTECTED] ___ 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
