Re: [gmx-users] XRAMA\environment variable\
Bio wrote: Hello sapiens, Thanks for ur previous suggestions. While we are trying to view ramachandran movie through xrama, we have got error as can't open display, set your DISPLAY environment variable.Let us come to know how to fix this problem.we are running GROMACS in winXP with cygwin. Thank You, Regards E.Elavazhagan. Do you have a running X server? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genbox
Li, Yun wrote: Thanks for getting back to me so quickly. I am following this tutorial: http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm It seems to be very straight forward. However, I can't overcome my problem. Here is the output from genbox: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 3.1.2 (-: You're using a prehistoric version of gromacs. I'm not sure how well that should work in Windows. It seems that there is a problem with file handling that could be OS specific (but none of the developers works with Windows). The output from genbox looks fine. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] XRAMA\environment variable\
Hello sapiens, Thanks for ur previous suggestions. While we are trying to view ramachandran movie through xrama, we have got error as can't open display, set your DISPLAY environment variable.Let us come to know how to fix this problem.we are running GROMACS in winXP with cygwin. Thank You, Regards E.Elavazhagan. -- Bio [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with genbox
Thanks for getting back to me so quickly. I am following this tutorial: http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm It seems to be very straight forward. However, I can't overcome my problem. Here is the output from genbox: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 3.1.2 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) c:\Program Files\Gromacs\bin\genbox.exe (-: Option Filename Type Description -cpbox.pdb Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa -cs spc216.gro Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb tpa -ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa -o water.pdb OutputGeneric structure: gro g96 pdb -p topol.top In/Out, Opt! Topology file Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 Generated table with 500 data points for COUL. Tabscale = 500 points/nm Generated table with 500 data points for LJ6. Tabscale = 500 points/nm Generated table with 500 data points for LJ12. Tabscale = 500 points/nm Going to determine what solvent types we have. There are 0 molecules, 12298 charge groups and 12298 atoms There are 0 optimized solvent molecules on node 0 There are 0 optimized water molecules on node 0 Grid: 18 x 14 x 20 cells Adding line for 2164 solute molecules to topology file (topol.top) Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -box vector 0 0 0 box size -nmolint 0 no of extra molecules to insert -tryint 10 try inserting -nmol*-try times -seedint 1997 random generator seed -vdwd real 0.105 default vdwaals distance -shell real 0 thickness of optional water layer around solute Reading solute configuration PROTEIN G (B1 IGG-BINDING DOMAIN) Containing 634 atoms in 80 residues Initialising van der waals distances... Opening library file C:\Program Files\Gromacs\share\top\vdwradii.dat Opening library file C:\Program Files\Gromacs\share\top\aminoacids.dat Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 3x2x3 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 3888 residues Calculating Overlap... box_margin = 0.315 Removed 2868 atoms that were outside the box Succesfully made neighbourlist nri = 20556, nrj = 531741 Checking Protein-Solvent overlap: tested 13099 pairs, removed 960 atoms. Checking Solvent-Solvent overlap: tested 120781 pairs, removed 1416 atoms. Added 2140 molecules Generated solvent containing 6420 atoms in 2140 residues Writing generated configuration to water.pdb Back Off! I just backed up water.pdb to ./#water.pdb.5# PROTEIN G (B1 IGG-BINDING DOMAIN) Output configuration contains 7054 atoms in 2220 residues WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file C:\Program Files\Gromacs\share\top\atommass.dat Volume : 75.6474 (nm^3) Density: 991.464 (g/l) Number of SOL molecules: 2164 Processing topology Back Off! I just backed up temp.top to ./#temp.top.5# Back Off! I just backed up topol.top to ./#topol.top.6# gcq#115: "A Lady Shaves Her Legs" (C. Meijering) Yun Li Assistant Professor of Chemistry Delaware Valley College 700 E. Butler Ave., Doylestown, PA 18901 (215) 489-2482 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genbox
Li, Yun wrote: Hi, I was very excited to discover Gromacs and decided to learn by following a few tutorials I found online. However, I ran into a problem: After filling up the simulation box with SPC water using genbox, the program backed up the topology file into another file with its name flanked by #, and left me with an empty topology file. Read carefully the output from genbox - I expect there's an error there that you've missed. Without knowing what had happened I went ahead and ran grompp, which exited with a fatal error, saying the number of atoms in the topology file does not match that of the coordinate file. I tried to use the backed up topology file, or to generate a new topology file using pdb2gmx, but ended up with the same error message. Grompp thinks there is no atom in the topology files. Well, of course it will, if the .top file is empty! Does anyone know what is going on? Also, water molecules don’t seem to appear in topology files. Does that matter? They get pulled in with the #include mechanism. The general structure of a .top file is a series of [ moleculetype ] sections, followed by a [ system ] section that describes the system as a set of the predefined molecules. For water, the [ moleculetype ] sections are contained in an .itp file that gets included by cpp. Your solute is in the .top file directly, in the usual case. Please read Chapter 5 fof the manual or more info. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME error in gromacs-3.3.1
Yuhui Li wrote: Hi, all I installed gromacs-3.3.1 recently and tested a system consisting only thress water molecules. When I use coulombtype = Cut-off, it works well, but if I use coulombtype = PME, there was a segmentation fault. I have checked the maillist archives and found that some people had the same problem in gromacs-3.3. From their instruction, the new pme.c file was tried and pme_order = 4 was set, but the problem is still there. Do you have idea about this problem? Actually, if you mean only "three" water molecules, the problem is likely to be that the fftw grid interpolation will fail if there is not at least one something per something (can't remember, check the archives if you care). Try doing a system of reasonable size. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME error in gromacs-3.3.1
Yuhui Li wrote: Hi, all I installed gromacs-3.3.1 recently and tested a system consisting only thress water molecules. When I use coulombtype = Cut-off, it works well, but if I use coulombtype = PME, there was a segmentation fault. I have checked the maillist archives and found that some people had the same problem in gromacs-3.3. From their instruction, the new pme.c file was tried and pme_order = 4 was set, but the problem is still there. Do you have idea about this problem? No, that problem is fixed in 3.3.1. I expect there is a problem with the installation of your fftw libraries.. I suggest you do a make clean, do configure again, and make install. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with genbox
Hi, I was very excited to discover Gromacs and decided to learn by following a few tutorials I found online. However, I ran into a problem: After filling up the simulation box with SPC water using genbox, the program backed up the topology file into another file with its name flanked by #, and left me with an empty topology file. Without knowing what had happened I went ahead and ran grompp, which exited with a fatal error, saying the number of atoms in the topology file does not match that of the coordinate file. I tried to use the backed up topology file, or to generate a new topology file using pdb2gmx, but ended up with the same error message. Grompp thinks there is no atom in the topology files. Does anyone know what is going on? Also, water molecules don't seem to appear in topology files. Does that matter? Thank you very much if you have read this much. Any idea what's going on. Your help will be greatly appreciated. Yun Li Assistant Professor of Chemistry Delaware Valley College 700 E. Butler Ave., Doylestown, PA 18901 (215) 489-2482 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PME error in gromacs-3.3.1
Hi, all I installed gromacs-3.3.1 recently and tested a system consisting only thress water molecules. When I use coulombtype = Cut-off, it works well, but if I use coulombtype = PME, there was a segmentation fault. I have checked the maillist archives and found that some people had the same problem in gromacs-3.3. From their instruction, the new pme.c file was tried and pme_order = 4 was set, but the problem is still there. Do you have idea about this problem? Thank you! -- Yuhui ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dipolar correlation function
Hi David Thanks for your reply. I want to calculate dipolar corelation function C(t) between proton and fluorine using the equation: C(t) = 1/4Σ[(3cos2θ(0)-1 )(3cos2θ(t)-1 )]/r(0)r3(t) (ref Fellar et al, JACS 121, 8963-64, 1999) where I have a proton i and total n fluorines. At time = 0, a proton-fluorine vector has a length r(0) and is oriented at an angle θ(0) relative to the z-axis. At a time t later in the trajectory the vector has length r(t) and is oriented at an angle θ(t) relative to the z-axis. Is there any way to get the plot of the average C(t) vs time (ps)? Thanks in advance Chiradip --- David van der Spoel <[EMAIL PROTECTED]> wrote: > chiradip chatterjee wrote: > > Hi gmx user, > > Is there any way in gromacs to compute dipolar > > correlation function between solvent atom and one > atom > > of my protein from trajectory data? I went through > > g_rotacf with -d option. But I think it gives > > rotational correlation function for linear > molecules > > by specifying two atoms (i,j) in the index file > that > > means two atoms i-j with a bond. > > Is g_dipole -corr is an option? > > please advice me. > > Chiradip > > > Please be more specific, what do you want to > compute? Please give an > equation. > > g_dipoles -corr computes a dipole vector from given > atoms (e.g. a water > molecule) and computes it's rotational > autocorrelation. > > g_rotacf may do what you need, you don't need a > bond, just a vector > between two atoms. However, if they diffuse apart > more than half a box > periodic boundary conditions will kick in and give > strange 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 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 > Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: free energy calculation & TI
Anirban and all, I am putting this on list since I don't want to make a full-time job out of answering free energy questions (although stay tuned for a more extensive tutorial) and hopefully I can avoid answering the same question more than once. I have seen your posts on gromacs mailing list regarding free energy calculation through TI and the need to partition the calculation into two steps : 1. change in VDW only 2. change in electrostatics only This isn't essential, but I think it's a good idea, at least in terms of efficiency. I was trying to run a free energy calculation run at lambda= and lambda=1 and I found that at lambda=1 my job blew up i.e. it showed LINCS warning and dumped stepxx.pdbs...could you tell me what might be the reason? This happened during stage 1 as mentioned above. In stage 2 the runs at lambda=0 and lambda=1 stops after sometime...seems there is some destabilizing forces. By stage 2, you mean changing electrostatics? It would be helpful if you could be more specific about the transformations you're doing, and how. Any number of things could be going on: (a) If, for example, you are doing things in a funny order (like first turning off van der Waals interactions, and then modifying the electrostatics) you may run into problems. (i.e. in that example, you have the possibility of bare charges with opposite signs overlapping with one another). (b) If you are changing Lennard-Jones interactions without using soft core, you can run into problems (c) If you don't do adequate minimization or equilibration, you can run into problems Overall, you are basically getting forces that are too large for your timestep for some particular reason. This could be related to the fact that you're doing free energy calculations, or it could have nothing to do with it. The basic solution is to figure out why you're getting such large forces, and fix it (if it's a problem); otherwise, reduce your timestep. I have also seen some posts where three steps are mentioned for free energy calculation..could you clarify on that ? It will be helpful if you quote them or point me to them; I don't have time to go through the archives to figure out what you're talking about or how it applies here. Sorry. I'm happy to help if you can be more specific. Sorry this stuff is so scattered through the archives. One thing on my to-do list is a "best practices" paper for free energy calculations (which will initially be a wiki page, before I publish it). When I pull that together, I will send an e-mail to the list so people can refer to that rather than having to dig through the archives. Best wishes, David thanks anirban Dr. Anirban Mudi Postdoctoral Fellow Biocomputing Group Department of Biological Sciences University of Calgary 2500 University Drive NW Calgary AB Canada T2N 1N4 (403) 220 6873 http://moose.bio.ucalgary.ca/ BE THE CHANGE YOU WISH TO SEE-> www.aidindia.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to implement dihedral restraints
I am not sure what you are asking since I believe that I have already given you this answer on the gromacs mailing list. http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html I certainly do not mind personal emails and I am happy to help, but there are three very good reasons to keep everything on the gromacs mailing list: 1. Answers may be read by people who disagree with portions of the answer -- such as Mark's suggestion that my system's stability using a dihedral restraint around 180deg was fortuitous and that you should redefine your dihedral to avoid that. http://www.gromacs.org/pipermail/gmx-users/2006-December/025089.html 2. I may not know the answer to your question but somebody else might. 3. The questions and answers are maintained for somebody else to search through years later. In fact, I don't know how to do exactly what you are suggesting. Do you mean that at every integration step the dihedral feels a pull toward it's 180deg opposite position? Or perhaps you want to do this (using phiAtTimeZero instead of phi on the right side of the equation): { X [ A (1+cos (nT-phi)) ] } - { (1-X) [ A (1+cos (nT-( phiAtTimeZero + 180 ))) ] } in place of the equation that you have written (below). In any event, if what you are asking is how to slowly change the umbrella then you could look into the afm pulling code and see if that is possible for dihedrals. Otherwise, you could do what I have suggested previously except that you should periodically stop and change the phi value of your dihedral restraint in the .top file and then grompp to get the updated tpr and then mdrun again. If you are asking how to use a cos function and thus be able to use 180deg... then you have me stumped. I also tried to do this but I think that it is not currently possible. If you do use my previous suggestion then please note that there is no guarantees that anything you do around a dihedral of about 180 using the dihedral restraint will work (since it is not a cos function). Therefore you should redefine the value. For example, I am working similarly with a chi1 dihedral. For this I have the options of N-CA-CB-CG or C'-CA-CB-CG. If I want N-CA-CB-CG to be at 180deg then one could instead require that C'-CA-CB-CG be at 60 deg (check this actual value for yourself though to ensure that I haven't slipped a sign or rotated the wrong direction... this is all from my memory of what I set up a while ago). Please don't hesitate to send another email to the list if you have some more questions on this topic. Quoting Prasad Gajula <[EMAIL PROTECTED]>: Dear Chris, Thanks a lot for your answer. I dont know if iam disturbing you. Iam very sorry for that. Hope you can help me to solve my prolem. i need to rotate a bond simultaneously from its present orientation to opposite orientation. my idea is like this... the dihedral angle formula is [ A (1+cos (nT-phi)) ] right. now, i want to do like this... { X [ A (1+cos (nT-phi)) ] } - { (1-X) [ A (1+cos (nT-( phi + 180 ))) ] } I change the value of X from 1 down to 0, say 0.9, 0.8,. that means i completely change the orientation of the bond. Now, my problem is how can i implement this special term in gromacs code only for my particular dihedral atoms say B-C (bonded atoms A-B-C-D) with simulation continues as usual normally for all other bonds. Please do not mind for sending mail to you personally. looking forward for your answer. Thank you very much! Best regards Prasad Message: 9 Date: Wed, 13 Dec 2006 15:54:28 -0500 From: [EMAIL PROTECTED] Subject: [gmx-users] How to implement dihedral restraints To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" For example, my peptide is rotating 50 degrees about a bond B-C, out of four bonded atoms A-B-C-D. I want to apply additional force on this dihedral(B-C) during my simulation(only for this particular atoms to make it rotate further till 180 degrees). All the remaining atoms in the peptide will have normal force as usual. May I ask you, how can I apply this in gromacs code. Any help will be appreciated! The current manual is good at describing what the options do for dihedral restraints, but (to my knowlegde) doesn't explain at all how to get the implementation up and running. Here is how I have done it based on searching the mailing list for answers. I suggest that something like this is added by way of example to the manual for future releases. Also, the manual is a bit unclear about whether this type of dihedral restraint is stable for use near 180deg. I have found that for my system everything appears to behave normally and as expected over the entire range of dihedral angles including 180deg. In your .top file: ; Include forcefield parameters #include "ffoplsaa.itp" ; Include topologies #include "myprotein.itp" [ dihedral_restraints ] ;
Re: [gmx-users] error after genion
Hi Carsten, You've included "ions.itp" twice... Note that this has crossed the mailing list recently and you could've found the answer by searching the archive. Tsjerk On 12/14/06, Carsten Baldauf <[EMAIL PROTECTED]> wrote: after i added ions using genion i get this error when i try to run grompp again: Generated 165 of the 1596 non-bonded parameter combinations Cleaning up temporary file grompphYfrXb --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CL- is redefined --- what am i doing wrong? cheers// carsten -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] error after genion
after i added ions using genion i get this error when i try to run grompp again: Generated 165 of the 1596 non-bonded parameter combinations Cleaning up temporary file grompphYfrXb --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CL- is redefined --- what am i doing wrong? cheers// carsten -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php