[gmx-users] REMD and demux.pl
Hi Gmx-users, i tried downloading the demux.pl script from the CVS repository. but i can't get thru, could anyone plz email me the script or just post it as a reply to this request, that would be a great help. thanks. arindam -- Arindam Ganguly Graduate Student VP(Chemistry Graduate Student Association-CGSA) Dept. of Chemistry, UMKC Phone:-816-419-1806 Email:- [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] REMD and demux.pl
Hi Mark, thanks for the prompt reply. i still have some questions. 1. Since i have to install the new version, should i make a clean install. 2. the version which i am currently using is *without* MPI, so this time i should be compliing or configuring it with MPI, as i understand. 3. if i want to run it on a cluster, does all the nodes need to have the same distribution of Linux(i am using Suse 10.1) and also does all nodes need to have GROMACS installed in all of them. i have gone through the mailing list , it looks like everyone is running it on cluster. could you please suggest any resource or tutorial for understanding the concepts and fundamental of running and performing molecular dynamics calculations in a cluster computing environment. thanks very much for your help. Arindam Ganguly ___ 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] REMD and demux.pl
Hi Gmx-Users, i am trying to run REMD for a protein, i looked at the mailing list regarding the discussion of REMD. it looks like veryone talking about the demux.pl perl script. i can;t find that in gromacs directory. can anyone plz provide me with the exact path of the script. i also checked the contibuted software sections, but no luck. any help is appreciated. thanks. arindam ___ 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] g_confrms_d options
Hi David,thanks again for the explanation. it makes a lot of sense now. any particular reference/s comes to your mind one should go thru regarding the same topic. it would really be a greta help. and thanks again. Arindam Ganguly ___ 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] g_confrms_d options
Hi David,Thanks for the reply. very well i agree with what you have to say. however in that case the answer which i am getting for other options claiming that the lsq fit say for backbone is 0.98732 so on ., are useless values. now again if that is the case shoukld i assume that native structure RMSD calculations using g_confrms_d is invalid. David i hope this question of mine making sense. plz clarify if i am missing something important. everyone is performing rmsd calculations on proteins, what is that i am doing wrong here. thanks.Arindam Ganguly ___ 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] g_confrms_d options
Hi Gmx-users,i am facing this problem i really don;t get it. i am trying to compare the rmsd of two strucures and when i use g_confrms_ d i the following options for the two structures Group 0 ( System) has 4276 elements Group 1 ( Protein) has 4276 elements Group 2 ( Protein-H) has 3260 elements Group 3 ( C-alpha) has 388 elements Group 4 ( Backbone) has 1164 elements Group 5 ( MainChain) has 1556 elements Group 6 (MainChain+Cb) has 1932 elements Group 7 ( MainChain+H) has 1932 elements Group 8 ( SideChain) has 2344 elements Group 9 ( SideChain-H) has 1704 elements Group 10 ( Protein) has 4276 elements Group 0 ( System) has 1198 elements Group 1 ( Protein) has 1053 elements Group 2 ( Protein-H) has 802 elements Group 3 ( C-alpha) has 96 elements Group 4 ( Backbone) has 288 elements Group 5 ( MainChain) has 385 elements Group 6 (MainChain+Cb) has 478 elements Group 7 ( MainChain+H) has 478 elements Group 8 ( SideChain) has 575 elements Group 9 ( SideChain-H) has 417 elements Group 10 ( Prot-Masses) has 1053 elements Group 11 ( Non-Protein) has 145 elements Group 12 ( NA) has 1 elements Group 13 ( HOH) has 144 elements Group 14 ( Other) has 145 elements Group 15 ( Protein) has 1053 elements i am able to calculate all options however for the "C-alpha" it keeps on giving me an error and the error is "You selected groups with different number of atoms." if you look at all other options also have different number of atoms, so howcome i don;t get this error message in other options. is there really problem here or i am missing something. pzl help thanks. Arindam Ganguly ___ 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] g_confrms_d
Hi Gmx-users in the manual of GROMACS 3.3 for the g_confrms , the manual states the following. " g confrms computes the root mean square deviation (RMSD) of two structures after LSQ fitting the second structure on the first one. " anybody has references to LSQ method ? thanks very much. Arindam Ganguly ___ 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] Beta Sheet folding simulation
Hi gmx-users,has anybody done a Beta Sheet folding simulation. any tutorials, references, books, input parameters, i hope i am not aksing for too much. i need help. i read thru gromacs manual and it talks about REMD. that's all. so need some more inputs from all of you out there. thanks. arindam ganguly ___ 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] *.xvg to jpeg/pdf/png
Hi gmx-users,i have a energy.xvg file, but i am not able to convert it to a jpeg, pdf or png format. in fact any cross platform format so that i can print out or send it for publications. any help in this regard is welcomed. thanks. arindam ___ 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] generate a pdb file
Hi GROMACS users,i have a 20 Amino acids peptide. i know the sequence. could you tell me how to generate a pdb file for the same so that it can be used for MD simulations using GROMACS. thanks.Arindam ___ 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] g_energy_d
Hi All,i am using the g_energy command to look for the info in simulation, when i give the command this is what is get :-bash-2.05b$ g_energy_d :-) G R O M A C S (-: God Rules Over Mankind, Animals, Cosmos and Such :-) VERSION 3.3.1 (-:-obvious details omiitted--- Select the terms you want from the following list- Bond Angle Proper-Dih. Ryckaert-Bell. Improper-Dih.LJ-14 Coulomb-14 LJ-(SR) Disper.-corr. Coulomb-(SR)Coul.-recip. Potential Kinetic-En. Total-Energy Temperature Pressure-(bar) Box-X Box-Y Box-Z VolumeDensity-(SI) pV Vir-XX Vir-XY Vir-XZVir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZYVir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar)#Surf*SurfTen Pcoupl-Mu-XX Pcoupl-Mu-YY Pcoupl-Mu-ZZ Mu-XMu-Y Mu-Z T-POP T-SOL Lamb-POP Lamb-SOL-my question is why don;t i see the number options for selection.i.e. why no number in front of each energy terms. is there any special boolean operator for this. plz let me know. thanks.Arindam Ganguly ___ 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] POPC simulation
Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly ___ 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] POPC simulation
Hi Jim i tried what you suggested and that is 1. yes the popc.gro file had all POPC residues truncated to POP, so i went ahead and changed the entries of popc.itp to pop, and i also did the same for topol.top file where inthe end you have to mention the number ofmolecules. but still the problem remains and it say again "LC3" atomtypes not found. so me still stuck. plz help. thanks. arindam ganguly On 5/24/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. CHARMM force field in GROMACS (Mark Abraham) 2. Re: Simulating crystalls (karamyog singh) 3. Position restrain (Alessandro Mattozzi) 4. Re: Position restrain (Xavier Periole) 5. Stange results of bonds fep (Oleg Stroganov) 6. POPC simulation (Arindam Ganguly) 7. Re: Simulating crystalls (Yang Ye) 8. Re: POPC simulation (Jim Fonseca) -- Message: 1 Date: Wed, 24 May 2006 23:22:14 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: [gmx-users] CHARMM force field in GROMACS To: Gromacs Users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, I am making available under GPL two perl scripts, one of which converts a CHARMM27 .prm file into the necessary .itp files for pdb2gmx to use to produce .top files, and another that massages that .top file into something that will produce a .tpr file that will get CHARMM energy & force evaluations. I have submitted it for inclusion on the GROMACS web page and hopefully it will appear there shortly. In the meantime, because I know there is interest in these scripts, if you want an email copy of the distribution that I hope will go up on the GROMACS web page, please email me off-list. Regards, Mark Abraham -- Message: 2 Date: Wed, 24 May 2006 17:06:52 +0200 From: "karamyog singh" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Simulating crystalls To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" I am trying to simulate a crystal too. I have a box size of .65 nm and there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm. I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I am trying to ask is, does GROMACS consider these as 2 different atoms placed at the respective positions or do the 2 atoms overlap? What could be the reason for the segmentation fault? Is it because the atoms are too close to each other? - Karamyog. On 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > > David van der Spoel wrote: > > Gale, Ella wrote: > > > >> > >> Thanks for the advice, but my force-field has no charges and hence no > >> coulomb potential, so I want the atoms to interact with itself via the > >> Van der Waals functions. I'm using 3.2.1 at the moment and there is no > >> option to use any of the Ewald summation techniques. Is this something > >> that has been added in the most recent version? > > > > Ewald variant are only for Coulomb so far. You can use a normal cutoff > > or a shifted cutoff. > > One or two of the early PME papers describe implementation details for > LJ PME, but I am not immediately aware of a modern MD code that > implements it. If you want it, shop around. > > 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 > -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060524/362cca6e/attachment-0001.html -- Message: 3 Date: Wed, 24 May 2006 17:13:09 +0200 From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Subject: [gmx-users] Position restrain To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi How should my posres.itp look like? Is there any template available? Thank R
[gmx-users] POPC simulation
Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just appended the files with the contents of the lipid.itp . now when i run grommp -v - -f em.mdp , it still says atom type "LC3" not found,. i can't understand why this mistake in fact taking place. popc.itp file the first 3 lines after [atom] in fact mentions LC3. so where is the mistake. plx help. thanks. arindam ___ 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] POPC simulation
Hi Steffen,Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :-#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp" #include "ffgmx2nb.itp"#include "ffgmx2bon.itp"however is still get the same message "Fatal error: Bonded/nonbonded atom type 'LP2' not found!". i forgot to mention one thing in my earlier mail that the ffgmx.atp file provided with originally from GROMACS , i replaced the contents of it by the contents present in the ffgmx.atp file present in the ffgmx_lipids folder as downloaded from the Gromacs website. my understanding is this shouldn;t cause the problem since the orinigal ffgmx.atp file ( as provided by gromacs) doesn;t contain all the atom types. in fact when i compared the both files i found that the ffgmx.atp file (from ffgmx_lipids folder ) has the following extra entries which were required for the lipid simulation. i am kind of confused as to where i am committig the mistake. plz help. thanks. Arindam GangulyHi Arindam,you've simply got to switch two lines in the *.top file: lipid.itp hasto be called by the topology before popc.itp, as it contains theinformation on atomtypes for GROMACS. So: #include "lipid.itp"#include "popc.itp"should work just fine.GreetingsSteffen ___ 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] POPC simulation
Hi gmx-users,i am trying to run a POPC simulation. this is what i have done. i downloaded the popc128apdb, lipid.itp , popc.itp files from the following website http://moose.bio.ucalgary.ca/index.php?page=Downloads then i also downloaded the ffgmx_lipids files from the gromacs website.i have copied the files from the ffgmx_lipids to /share/top folder. in the popc.top (popc topology) files i have mentioned it to include all of these as ; Include the force field parameters #include "ffgmx.itp"#include "popc.itp"#include "lipid.itp"#include " ffgmx2nb.itp"#include "ffgmx2bon.itp"; Include water topology#ifdef FLEX_SPC#include "flexspc.itp"#else#include "spc.itp"#endif[ system];POPC + Water EM [molecules]; name number POPC 128 SOL 2460 when i give the following command"grompp -f em.mdp -c popc128a_b4em.gro -p popc.top -o popc.tpr"it gives me an error saying "atom type LP2 not found". however the lipid.itp and popc.itp allhave the declaration for LP2 atom type. but still why there is an error. plz help. thanks.Arindam ___ 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] Villin Benchmarks grompp error (Please Help)
Hi GROMACS users,sorry please disregard the earlier message realised it was too long.i am new to GROMACS. i have been trying to run the Villin Benchmarks using the conf.gro, grompp.mdp and topol.top file provided with the benchmark folder. i giving the grompp command as follows grompp -f grompp.mdp -c conf.pdb -p topol.top -o em.tprand after that i get this message, Fatal error:number of coordinates in coordinate file (conf.pdb , 9389) does not match topology (topol.top, 0)--- "The Candlelight Was Just Right" (Beastie Boys) After going through the GROMACS mailing list I realised this is a classical mistake which everyone makes. that's fine, but even after making the changes as pointed out by many users that check the number of atoms in topol.top and conf.gro file i am still getting the same error.i am providing in the email conf.gro and the topol.top file. can anyone of you plz suggest as to what is wrong. where i have to make the changesinorder for me to run the simulation.thanks.the file are provided below.Arindam Gangulyconf.groVILLIN in water 9389 1MET N 1 2.185 2.903 2.012 -0.4460 -0.1439 0.3043 last line of the conf.gro file3036SOL HW2 9389 4.069 1.007 3.359 0.8423 -0.6670 -0.9379 5.02729 4.73973 4.10445 0.0 0.0 1.67574 0.0 -1.67574 2.36986 topol.top file[ system ]; NameVILLIN in water[ molecules ]; Compound #molsProtein 390SOL 8999 ___ 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
