Re: [gmx-users] Selecting Nodes While Running Parallel Mdrun
hi, On Tuesday 25 April 2006 07:44, Shankar Prasad Kanaujia wrote: Dear Gromacs Users, I am installing parallel version of gromacs on linux cluster, but I do not want to use all the nodes for my simulation. Is there any way to select some specific nodes for simulation ? Will I have to specify the nodes while installing or I would be able to select the nodes after installation according to my requirement ? What are the necessary files to be edited for the same ? You have to install a batch processing and resource management system, there are several around like openpbs (http://www-unix.mcs.anl.gov/openpbs/), maui and torque ... also there s a solution from sun/ sgi afaik the only free solution is openpbs and it will work for small installations without high requirements. if you want to run it parallel you have to install mpich and lam. Also a shared filesystem for all this nodes would be nice (easiest nfs also afs or any other shared filesystem like clusterfs). Thanks, Shankar Prasad Kanaujia ___ 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] LINCS deviation
hi, On Monday 24 April 2006 21:12, Ashutosh Jogalekar wrote: Hello I am simulating a regular seven residue peptide: HHQALVFFA, in the form of a beta sheet with five strands. The EM went ok. The structure looks ok. But I am still getting the error about the LINCS constraint deviation during the posit. restr. MD. Could someone suggest what I could do to get rid of the problem? dt= 0.002 nsteps= 1 constraints= all-bonds tau_p= 1.0 have you solved your system, when yes try a position restraining of water: define = -DPOSRES_WATER or of your backbone Thanks Ashutosh Jogalekar Emory University ___ 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] Gromacs 3.3.1 MPI/Itanium 2 fails to build
Hi Matt, For reference, please try: gcc, without mpi icc, without mpi If those two also fail, go to src/gmxlib/nonbonded/ nb_kernel_ia64_single and issue make nb_kernel010_ia64_single.lo to see what happens. My first guess would be that the mpicc wrapper scripts are broken and don't handle assembly files correctly. In that case you might have to link in the MPI libraries manually - check the FAQ. Cheers, Erik On Apr 25, 2006, at 12:54 AM, [EMAIL PROTECTED] wrote: Yes, I did make distclean before configuring with MPI enabled. Matt Ernst Washington State University [EMAIL PROTECTED] a écrit : Hello, I have successfully built Gromacs 3.3.1 under Linux/Itanium 2 with the following configure options: ./configure -with-fft=fftw3 --without-x --prefix=$HOME/gmx331 When I enable MPI, the build fails: ./configure -with-fft=fftw3 --without-x --prefix=$HOME/gmx331 -- enable-mpi;make Have you made a make clean (or make distclean) before doing the second configure ? If not, its the way to try first :-) Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http:// migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selecting Nodes While Running Parallel Mdrun
Hi, On Apr 25, 2006, at 8:47 AM, Florian Haberl wrote: hi, On Tuesday 25 April 2006 07:44, Shankar Prasad Kanaujia wrote: Dear Gromacs Users, I am installing parallel version of gromacs on linux cluster, but I do not want to use all the nodes for my simulation. Is there any way to select some specific nodes for simulation ? Will I have to specify the nodes while installing or I would be able to select the nodes after installation according to my requirement ? What are the necessary files to be edited for the same ? You have to install a batch processing and resource management system, there are several around like openpbs (http://www-unix.mcs.anl.gov/ openpbs/), maui and torque ... also there s a solution from sun/ sgi afaik the only free solution is openpbs and it will work for small installations without high requirements. Cluster resources provide great free tools in Maui (scheduler) and Torque (batch system build on OpenPBS). They are distributed with the (also free) Rocks linux cluster distribution, and we're using them quite successfully on a 600-CPU cluster in Stanford :-) Cheers, Erik ___ 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] Doubt in Distance Restraints
Hi Raja,Yes, that's the idea. So funct (which is 2 now) is changed to 6, but you will still need to specify the equilibrium bond length and the force constant. The bond length can be chosen from the crystal structure, if no other information is available, and the force constant isn't too important if the purpose is too keep the things together. But there must be some parameters for Fe(II)-ligand bonds lying around somewhere. Cheers,TsjerkOn 4/25/06, raja [EMAIL PROTECTED] wrote: Hi Mr.Tsjerk,Thanks for your reply and I checked manual based on yoursuggestion. I just want to make it sure, Is it what the manualsays while adding type 6 bond that isto edit the protein.top file under [bond] section so as to depict harmonic interactionbetween metal and ligating atoms.###[ bonds ];aiaj functc0c1c2 c3 473437242 473428392 473428722#Where 4734 is Fe(II) atom and 3724,2839,2872 are respective metalchelating atoms of protein.Is it ok ? With thanks !B.NatarajOn Thu, 20 Apr 2006 10:11:34 +0200, Tsjerk Wassenaar[EMAIL PROTECTED] said: Hi Raja, You may be better off just adding bonds. I believe there was a bond type (type 6) which was especially useful (intended?) for keeping metals bound to a protein. Cheers, Tsjerk On 4/20/06, raja [EMAIL PROTECTED] wrote: Dear all, My intention is to restrict Fe(II) in active site by distance restraint protocol. Fe(II) is ligated by three amino acides' polar atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of ASP. The following is the disres itp file I used (copied from manual3.3). where I edited the atom number of aminoacids(3724,2839,2872) and Fe(II) as 4734. # disres.itp # [ distance restraints ] ; ai ajtypeindextype' low up1 up2 fac 37244734 1010.02.090.4 1.0 28394734 101 0.02.250.4 1.0 28724734 1010.02.180.4 1.0 I do not understand the meaning of up2 and fac so I left with 0.4and 1.0 as such as found in manual. In mdp file I added the following the commands ## full.mdp ## define = -DDISRES disre= Simple ### I expected these modifictions will restrict but those distances are not restraintedwhy ? Kindly explain me that wheather I need to change any other parameter . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - IMAP accessible web-mail ___ 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, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 --raja[EMAIL PROTECTED]--http://www.fastmail.fm - I mean, what is it about a decent email service?___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ 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] Imaging in PBC simulations -summary
Dear Jochen and Tamas, thanks for your replies. I tried both, the trjconv -fit postprocessing and setting comm_mode for mdrun and actually only the latter worked fine. In the former, protein drifts toward the box side and jumps out for some frames, leaving its bound ions inside the box. Better to remove translation during the run. All the best, Martin Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and not set. I watch the movie in VMD, loading first a starting gro and than the trr. The problem is that the protein creeps out of the box (the same happens when using ngmx). I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric), groups for fitting: protein or system. But in any case, the result is the same. Could you please advice me how to solve this? Whether it is better to include some parameter for mdrun or to post-process in a different way? Looking forward to hearing from you. Yours sincerely, Martin Lepsik You can either use comm_grps = Protein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- -- Martin Lepsik, Ph.D. Laboratoire de Dynamique Moléculaire (LDM) Institut de Biologie Structurale 41, rue Jules Horowitz 38027 Grenoble Cedex 1, France tel: +33-4-3878-4780 e-mail: [EMAIL PROTECTED] ___ 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] System equilibration and interaction energy
Dear Gromacs users, I have two queries : 1. I am doing simulation for a protein (156 residues ) with a sugar. Out of 156 protein resiudes i have restrained 130 residues and rest part i have kept free. My doubt is that when we can say that system has equilibrated? if on the basis of rmsd then i dont feel it would be advisable to look the rmsd of protein because major part i have restrained, if i consider sugar rmsd then i can see a kind of periodicity in the rmsd. if i look the rmsd of the system then it seems to be stablized at 4.5nm. if i look the potential energy of the system then from the begining itself it seems to be equilibrated with a fluctuation of ~700kj/mol. I guess that may be because of very high contribution from the solvent. For nearly 26000 atoms i have done the simulation upto 4 ns. So i would just like to know that what is the best way to define system equilibration when a major part is restrained. 2. my second question is about caluclation of the interaction energy betwen the protein and the ligand. one possible way seems to be calculate all the energy pairs given by gromacs with ligand and protein (ljsr, ljlr, lj14 and for coulombs) and sum it or do i need to do two more simulations, one with protein alone in the same box size with same number of water molecules and other with the ligand alone and then substracting the sum of potential energies of independent simulations from the protein-ligand energy? any suggestion would be highly appreciated thanks ___ 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] System equilibration and interaction energy
Dear Gromacs users, I have two queries : 1. I am doing simulation for a protein (156 residues ) with a sugar. Out of 156 protein resiudes i have restrained 130 residues and rest part i have kept free. My doubt is that when we can say that system has equilibrated? if on the basis of rmsd then i dont feel it would be advisable to look the rmsd of protein because major part i have restrained, if i consider sugar rmsd then i can see a kind of periodicity in the rmsd. if i look the rmsd of the system then it seems to be stablized at 4.5nm. ___ 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] Selecting Nodes While Running Parallel Mdrun
If you are using Lam/mpi you have to lamboot as much as nodes as you want in the hostfile, you must specify the number of nodes as well as their IP. Cesar Shankar Prasad Kanaujia escribió: Dear Gromacs Users, I am installing parallel version of gromacs on linux cluster, but I do not want to use all the nodes for my simulation. Is there any way to select some specific nodes for simulation ? Will I have to specify the nodes while installing or I would be able to select the nodes after installation according to my requirement ? What are the necessary files to be edited for the same ? Thanks, Shankar Prasad Kanaujia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comm-mode = Angular
Hi All, Dose anyone know any literature regarding comm-mode = Angular option? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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] parallel gromacs
hello, i would like to run gromacs in parallel on a single pc with 4 processors. as far as i understand it, this is not possible using mpi. is that correct? and if so, what do i have to use instead? thanks, marc ___ 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] parallel gromacs
Hi, It's certainly possible to do with MPI. LAM will for instance automatically detect the number of available CPUs, and uses fast shared-memory communication within each node. Cheers, Erik On Apr 25, 2006, at 4:55 PM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: hello, i would like to run gromacs in parallel on a single pc with 4 processors. as far as i understand it, this is not possible using mpi. is that correct? and if so, what do i have to use instead? thanks, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] parallel gromacs
This should be entirely possible with MPI. Depending on which MPI implementation you are using, you would define your machine pool to be 4 instances of the same machine. The documentation for both LAM and MPICH provide documentation on how to do this as a default configuration. Cheers, Shawn Pittsburgh Supercomputing Center Senior Scientific Support Specialist [EMAIL PROTECTED] Carnegie Mellon University Pittsburgh Supercomputing Center Rm #369 Pittsburgh, PA 15213 tel: 412-268-4635 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, April 25, 2006 10:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] parallel gromacs hello, i would like to run gromacs in parallel on a single pc with 4 processors. as far as i understand it, this is not possible using mpi. is that correct? and if so, what do i have to use instead? thanks, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ffG43a2 and vdw
Hi In the manual (page 81) it mentions that when using a Gromos96 ff the LJ cut-off should be set at 1.4nm or more, I have been using 1.0nm, should this cause many problems? Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ 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] comm-mode = Angular
Naser, Md Abu wrote: Hi All, Dose anyone know any literature regarding comm-mode = Angular option? This works,however, only with simulations in vacuum. In a water box you get overlaps at the box boundaries from angular rotations done by the comm-mode = Angular option resulting in lincs warnings... cheers, jochen With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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 -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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] EM comparison
Hi all ! I was doing EM for a bilayer. While using the mdp file containing only the energy minimization terms my energy is minimized but i get the following : Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 111 steps, but did not reach the requested Fmax 100. Potential Energy = -5.2422903e+05 Maximum force = 3.8640459e+03 on atom 18141 Norm of force = 7.6843672e+04 What are the implicationsof Fmax 100 in my case. Also if i modify the mdp file and increase the terms to contains the temp and pressure coupling terms my energy comes out to be the same but at the same time my Fmax also converges to 100. WHY SO? Please comment ! Thanks in ADVANCE. Kushal Seth ___ 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] Gromacs-3.3.1 installation
Hi Dr. David I am trying to install Gromacs-3.3.1 on the following platform now: redwood r0914/gromacs-3.3.1 uname a Linux redwood 2.6.5-7.244-sn2 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ia64 ia64 ia64 GNU/Linux Everything went okay, but, I got the following error during make install make did not gave any error /usr/bin/install: `./g_sham.1' and `/work1/r0914/gromacs-3.3.1/man/man1/g_sham.1' are the same file /usr/bin/install -c -m 644 './make_edi.1' '/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1' /usr/bin/install: `./make_edi.1' and `/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1' are the same file make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/work1/r0914/gromacs-3.3.1/man' make: *** [install-recursive] Error 1 __ Can you suggest how to fix this? Regards Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: [EMAIL PROTECTED] Tel: 662-915-1286 (office); Web: www.olemiss.edu ___ 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] System equilibration and interaction energy
[EMAIL PROTECTED] wrote: Dear Gromacs users, I have two queries : 1. I am doing simulation for a protein (156 residues ) with a sugar. Out of 156 protein resiudes i have restrained 130 residues and rest part i have kept free. My doubt is that when we can say that system has equilibrated? You will never be able to say the system is equilibrated - only that it may be equilibrated subject to the restraints. if on the basis of rmsd then i dont feel it would be advisable to look the rmsd of protein because major part i have restrained, if i consider sugar rmsd then i can see a kind of periodicity in the rmsd. if i look the rmsd of the system then it seems to be stablized at 4.5nm. if i look the potential energy of the system then from the begining itself it seems to be equilibrated with a fluctuation of ~700kj/mol. I guess that may be because of very high contribution from the solvent. For nearly 26000 atoms i have done the simulation upto 4 ns. So i would just like to know that what is the best way to define system equilibration when a major part is restrained. You have the same methods available to guide your guesses as for unrestrained MD - check that observables like total energy, density, position RMSD (for systems expected to be in a PE minimum) are doing sensible things. Since the information content of the restrained atoms is low, you may like to exclude them from the maths. 2. my second question is about caluclation of the interaction energy betwen the protein and the ligand. one possible way seems to be calculate all the energy pairs given by gromacs with ligand and protein (ljsr, ljlr, lj14 and for coulombs) and sum it or do i need to do two more simulations, one with protein alone in the same box size with same number of water molecules and other with the ligand alone and then substracting the sum of potential energies of independent simulations from the protein-ligand energy? Your second method would be totally weird. If you are using an NVT ensemble, you will now have a different density, so your solvent will be doing different things interacting with itself and the remaining solute such that there's no reason to expect energy additivity. If NPT, the system will contract and there's still no such reason. I believe the first method is the accepted practice. The interaction energy is purely through-space in the absence of bonding, and so only the LJ and Coulomb terms contribute... thus they are all you need to consider. 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
