Re: [gmx-users] How to construct mixed lipid bilayer
Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote: Dear All, can anyone tell me how to construct mixed lipid bilayer in gromacs id possible also provide me the command to construct the mixed bilayer Thanks in advance Nikhil -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to construct mixed lipid bilayer
Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :) On Nov 13, 2013 7:23 PM, Arun kumar V arun.tar...@gmail.com wrote: Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote: Dear All, can anyone tell me how to construct mixed lipid bilayer in gromacs id possible also provide me the command to construct the mixed bilayer Thanks in advance Nikhil -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Restarting a simulation after replacing an empty md.trr file
Dear Gromacs users, I am running a 50ns simulation of a protein having nearly 700 residues on 60 threads (Gromacs 4.6.3). At one point i got a disk space problem, so i have deleted the md.trr file and created an empty md.trr file. when i tried to restart the simulation from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt 100 ] i am getting a note and an error as fallows Reading checkpoint file md.cpt generated: #PME-nodes mismatch, current program: 100 checkpoint file: 60 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. ... Source code file: checkpoint.c, line: 1767 Fatal error: Can't read 1048576 bytes of 'md.trr' to compute checksum. The file has been replaced or its contents has been modified. please help me in overcoming this problem. Thanking you. -- Arun Kumar Somavarapu Project-JRF Dr. Pawan Gupta's lab Protein Science and Engineering Dept, Institute of Microbial Tecnology, Sec 39-A, Chandigarh - 160036. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] do_dssp segmentation fault
Dear all, Iam trying to generate secondary structure plot through do_dssp program, but there was an error like segmentation fault Reading file md.tpr, VERSION 4.0.7 (single precision) Reading file md.tpr, VERSION 4.0.7 (single precision) Segmentation fault (core dumped) bash-4.1# can anybody please say what it means and how to solve it Regards, -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Dear friends, i had a problem while running the of protein-ligand complex simulation, in which i have generated the ligand toplogy by using online Prodrg server and iam using gromos 96.1froce field. there was an note and an error during minimization NOTE 2 [file trp.top]: The largest charge group contains 15 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 223Protein residues There are: 1 Other residues There are: 25853 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 161838.00 Largest charge group radii for Van der Waals: 0.790, 0.356 nm Largest charge group radii for Coulomb: 0.790, 0.399 nm WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (1.188798) is larger than rlist (1.00) i am using the mdp file the one that i copied from gromacs protein-ligand tutorial can any one please explain these errors so that i can go farward in my work. and i have a doubt, as there are other updated forcefields, how much reliable is the gromos 96 ff -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
hi justin, as u said i understand that there is inconsistency in the charges and charge groups of PRODRG server itself. can u suggest me any other softwares that i can rely on for this work. Thanking you. On Tue, Nov 15, 2011 at 7:48 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul) 2. RMSD (shahid nayeem) 3. Problem during GROMACS 4.5.5 installation (sai nitin) 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul) 5. Re: RMSD (Gianluca Santoni) 6. Re: RMSD (felmer...@uchile.cl) 7. Re: Positive potential energy for TFE solvent (Harpreet Basra) -- Message: 1 Date: Tue, 15 Nov 2011 06:40:31 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ec24faf.5050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed arun kumar wrote: Dear friends, i had a problem while running the of protein-ligand complex simulation, in which i have generated the ligand toplogy by using online Prodrg server and iam using gromos 96.1froce field. there was an note and an error during minimization NOTE 2 [file trp.top]: The largest charge group contains 15 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 223Protein residues There are: 1 Other residues There are: 25853 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 161838.00 Largest charge group radii for Van der Waals: 0.790, 0.356 nm Largest charge group radii for Coulomb: 0.790, 0.399 nm WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (1.188798) is larger than rlist (1.00) i am using the mdp file the one that i copied from gromacs protein-ligand tutorial can any one please explain these errors so that i can go farward in my work. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb and i have a doubt, as there are other updated forcefields, how much reliable is the gromos 96 ff The problem is not the reliability of Gromos96, but the reliability of PRODRG. Please read the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to understand why you should almost certainly never use the charges and charge groups that PRODRG creates. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 2 Date: Tue, 15 Nov 2011 17:53:19 +0530 From: shahid nayeem msnay...@gmail.com Subject: [gmx-users] RMSD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAB_3DJa8m-jooJb=cmscmrds8ja-rzdm7gmdm+oku7s7qem...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2015/c99194fb/attachment-0001.html -- Message: 3 Date: Tue, 15 Nov 2011 14:03:03 +0100 From: sai nitin sainit...@gmail.com Subject: [gmx-users] Problem during GROMACS 4.5.5 installation To: gmx-users@gromacs.org Message-ID: cagjtc4nwdf9a2v9t8eep1jma+s4kecoa6p8rnl6vnm_m7hq...@mail.gmail.com Content-Type: text/plain
[gmx-users] simulation at higher temperatures gmx-users Digest, Vol 88, Issue 167
hi justin, I accept with u that simulation will not complete in 3ns, but as iam trying simulation at 400k for the first time i just kept it for 3ns to see how it will be. and for checking conformational changes i saved the structures for each 100ps from the trajectory (is it a correct procedure for that.?) and is it possible to give explanation for the parameters and forcefield that we need to fallow for higher temperature simulations..? On Mon, Aug 29, 2011 at 7:24 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: OPLS-AA Unknown Atomtype (Justin A. Lemkul) 2. Error found on grompp - energy minimization (ITHAYARAJA) 3. Re: Error found on grompp - energy minimization (Mark Abraham) 4. Re: gromacs question topologie (Justin A. Lemkul) 5. Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED] (Pablo Englebienne) 6. simulation at higher temperatures (arun kumar) 7. Re: simulation at higher temperatures (Justin A. Lemkul) -- Message: 1 Date: Mon, 29 Aug 2011 06:41:32 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e5b6cdc.8000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] simulation at higher temperatures
Hi friends, As a part of my work i have to do simulation at higher temperature (400K or more) to study the folding, unfolding and stability of protein, for that i kept simulation for 3ns at 400k (400k temperature both in equilibration and production) keeping all the other parameters as usual (time step 2fs, explicit solvent model SPC, equilibration with NVT and NPT ensembles for 100ps each ). the simulation was completed but , 1. in trajectory i found that protein is comming out of the box (cubic box -d 1.0) i think may be the box size was not sufficient (and i know that when we increase the temperature the velocity of atoms will increase). 2. when i save the structure with minimum energy and saw in pymol i found the side chains, hydrogens was broken through out the protein. 3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the conformational changes by playing it as a movie in pymol , but i found a single conformation was just shaking through out the movie (this is happening in normal simulation also) later i read in gmx user problems that most of the force field parameters are calculated at room temperature, so in that case what are the parameters and forcefield that we need to fallow for higher temperature simulations. so can any one please takes time to explain this, it would be helpful for me to study further. Thanking you. with regards -- Arun Kumar Somavarapu Center for Bioinformatics Pondicherry University Kalapet Puducherry-605014 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of only Lipid Bilayer
On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: Arun kumar V wrote: Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file. If by be careful you mean don't use this topology, I'll agree :) The Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1, given by PRODRG) fall far short of reproducing lipid properties. That, and the charges assigned by PRODRG for lipids will not resemble any known parameter set, requiring a complete re-write of this topology. You could use PRODRG to build the molecule, but there are a number of other programs that can do that as well (see the Gromacs site for a list). To the original post: What lipid are you looking to simulate? Many pre-equilibrated lipid bilayers are available in the public domain, along with suitable paramters, saving you a lot of work in building these systems. They can be tricky. -Justin @Justin I agree with you. Currently I am not actively involving with gromacs simulations but planning to involve. I have not been to GROMACS website from long time. In fact the version I have used last time is gromacs 3.3(almost 2 years back). There is lot of progress ofcourse. Thanks, Arun Arun Saumya wrote: Hi all, Well, I have been trying to make lipid bilayers using genconf of gromacs from a single lipid molecule. Can anyone tell me how to proceed with the simulation of lipid bilayers starting with a single lipid molecule? How can I obtain the .pdb file for a lipid? Is there any manual that describes the procedure using Gromacs? Hoping for some inputs. Regards Saumya -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation of only Lipid Bilayer
Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file. Arun Saumya wrote: Hi all, Well, I have been trying to make lipid bilayers using genconf of gromacs from a single lipid molecule. Can anyone tell me how to proceed with the simulation of lipid bilayers starting with a single lipid molecule? How can I obtain the .pdb file for a lipid? Is there any manual that describes the procedure using Gromacs? Hoping for some inputs. Regards Saumya -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Forming a micelles
Dear Lin, Actually I chose the concentration randomly and viewed the pictures. I used united atom force field. Surfactant is Behenyl trimethyl ammonium chloride and co surfactant is stearyl alcohol. I did carry out simulations for 4 different concentrations. I did not carry out simulations to find out what is CMC. For the system size I mentioned... I carried out simulations for 600 ps from random configurations. And then I checked pictures and also checked energies and other properties. And once again started from the final configuration of the first simulation for next simulation (another 600 ps). Similar way Third simulation.. In the last 600 ps I observed Micelle formation and also energies and properties are constant over some 300 ps. Only through visualization only I observed micelle formation. With regards, Arun On Wed, Sep 24, 2008 at 10:45 PM, Chih-Ying Lin [EMAIL PROTECTED]wrote: Hi Would you please say more about your system? How do you design / decide your simulation size of 100 surfactants +100 co-surfactants + 4000 water molecules?? How many surfactants will form a micelle? How many atoms does one surfactant have? How many atoms does one co-surfactant have? Do you start from the critical micelle concentration? You mentioned that it took 3 x 600 ps to see the micelles. Do you mean that you have 3 computers to do the parallel simulation? How long does it take to simulate 600 ps? Do you visualize the whole 600 ps-image and SEE the micelle? Or, other technique to KNOW the surfactants forming the micelles without visualizing the system? Thank you Lin Hello there... I carried out simulations of mixture of cationic surfactants, fatty alcohols and water with various ratios of surfactant/alcohol. Usually for a system of 100 surfactants +100 co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the micelles and other structures forming from random configurations. Arun -- Arun Kumar ___ 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] Relationship between the spetide.gro file and the #spetide.gro.1#?
Hai. If your working directory contains a file named already speptide.gro, when u run another simulation for which the output (final coordinates) is also speptide.gro, then the previous file will be backed up as #speptide.gro.1# . Similarly if u run another simulation then the speptide.gro file will be backed up as #speptide.gro.2# . It applies to every file in ur working directory. Hope u understood.. On 8/14/07, huifang liu [EMAIL PROTECTED] wrote: Hi, I am a new learner of Gromacs.I want to kown what relationship between the spetide.gro file and the #spetide.gro.1# file is and how to see the content of the #spetide.gro.1# file. Hope to get your help! ___ 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 -- Arun kumar.V M.E Chemical Engineering ___ 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] CVS code needed
Dear Erik, Thank you for the link Kumar On 7/22/07, Erik Lindahl [EMAIL PROTECTED] wrote: I put a recent copy (friday) at http://lindahl.sbc.su.se/outgoing/aatto/ Cheers, Erik And yes... we should get a nightly-snapshot system running... :-) On Jul 22, 2007, at 4:08 PM, Kumar V wrote: Hai all, Our campus network is behind firewall because of which I cant use CVS pserver.. And I dont know any alternative how to get current CVS development code. Can anyone of you tell me how to get gromacs current CVS source code?? I will be grateful even if anyone of u send me tar.gz file. Thanks in advance Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical Engineering ___ 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] Continuing runs that stopped
There are two ways of doing this 1) using grompp (check man page) 2) using tpbconv(easier) check man pages for tpbconv.. On 6/13/07, michelle yap [EMAIL PROTECTED] wrote: Hello, I was doing an MD simulation and I need to restart my PC because of some technical problems that occurred in the process. Is there a way of continuing the simulation without having to start anew? Thank you! _ Search from any Web page with powerful protection. Get the FREE Windows Live Toolbar Today! http://toolbar.live.com/?mkt=en-ph ___ 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 -- Arun kumar.V M.E Chemical ___ 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] glibc error with g_density (only for some cases)
Dear David, I will check the reproducibility of the result once again. And then I will submit the bugzilla with all inputs I used for these simulations. Regards, Arun On 5/19/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. gcc 4.0.1 should be fine as far as I know. You are welcome to submit a bugzilla with input that reproduces the problem. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ 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] glibc error with g_density (only for some cases)
Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ 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] initial configuration problems and energy minimization
Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counterions) and also am able to simulate... But when I increase the number of surfactants or co-surfactants. Even the energy of the system initially is a big negative. When I start true simulation, Potential energy is becoming positive...and ultimately box is exploding [xtc error or some times ci error].. still I tried to minimize the energy of initial configuration, but I am getting the same error. Below I describe the steps i took to do simulations 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and co-surfactant(str.gro) in Vaccum 2)Generate a system of 100 surfactnats(includes counterions), 20 co-surfactants and 1000 waters by using packmol(random) 3)Minimize the whole system until potential will become a reasonable negaive 4)With that minimized structure I run simulation but always the box is exploding My simulation is successful when the no of surf and co-surf are 15+15 For this successful simulation Initially i am conducting a NVT simulation with 0.01 fs timestep at 100K temp and then another NVT at desired temp(300K) and then NPT with 2fs timestep I don't know why I am unable to conduct with more no. of surfactants in water. I tried the samething for a bilayer initial configuration also(generated by packmol), but getting same error Is there any solution to solve this??? I already checked archive lot of times but i am unable to find anything relevant. I think its not that much related to gromacs.. But i need help to solve this problem I can give any more details if it is needed. Thanks in advance -- Arun kumar.V M.E Chemical, IISc ___ 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] initial configuration problems and energy minimization
Hi Mark. Thanks for your suggestions I will use your suggestions to solve the problem. And then I will reply here about the outcomes. Regards Arun On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counterions) and also am able to simulate... But when I increase the number of surfactants or co-surfactants. Even the energy of the system initially is a big negative. When I start true simulation, Potential energy is becoming positive...and ultimately box is exploding [xtc error or some times ci error].. still I tried to minimize the energy of initial configuration, but I am getting the same error. Below I describe the steps i took to do simulations 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and co-surfactant(str.gro) in Vaccum 2)Generate a system of 100 surfactnats(includes counterions), 20 co-surfactants and 1000 waters by using packmol(random) 3)Minimize the whole system until potential will become a reasonable negaive 4)With that minimized structure I run simulation but always the box is exploding My simulation is successful when the no of surf and co-surf are 15+15 For this successful simulation Initially i am conducting a NVT simulation with 0.01 fs timestep at 100K temp and then another NVT at desired temp(300K) and then NPT with 2fs timestep This looks pretty reasonable. You should check visually that packmol is not generating a conformation with atoms that are too close together. You can try using position restraints during your equilibration steps, and equilibrating for longer. The explosion is almost certainly happening because atoms are too close at some point, and these leads to huge energies. If your density is wrong for your NVT, then relaxing to NpT too quickly can cause this sort of problem too - use a large tau_t, or generate a box closer to the right size initially. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ 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] glibc error with g_density (only for some cases)
Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted It is giving a empty density.xvg file I get same error if I use g_density -b 1000 I checked the reproducibility of the error.. I am getting it always(I mean I am using g_density once again again, Not simulating the system once again again) But when I use g_density -b 1500 or more I am getting densities normally. Actually i am doing simulations at 4 different temperatures. But I am getting the error only for three temperatures For one temperature Every thing is fine.. Gromacs version I am using is : 3.3.1 I checked the archives and in google I found a similar error in archives for make_ndx After checking in google I came to know that its a common bug with glibc package of different versions. Now i want to know is there anything wrong in my simulations(possibilities) and also how I can rid of these errors. Thanks and Regards -- Arun kumar.V M.E Chemical, IISc ___ 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: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Hai Tsjerk, David, Mark and others, Thank you for all your responses. I had been successful in setting up simulation and also in understanding what David and Mark told. As Dr. David suggested, I started EM for single surfactant in vaccum and successful in minimizing the energy. Also I did EM for my co-surfactant stearyl alcohol and had been successful. Then I started minimizing the energy of a system of 500 waters+ 1 cationic surf+ 1 fatty alcohol. It also worked fine. And I started true dynamics(MD) of the bulk system and had been successful. I think all these posts will be useful for others who start gromacs with these kind of systems. So for me, Now the only problem is getting correct forcefield for my surfactant system to get good physical properties. I will post the topology for my surf and co-surf when I will be successful in doing that. Thanks and Regards Arun Kumar On 5/6/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Hi Tsjerk and others, I tried to simulate one surfactant and one chloride ion in 500 waters and got similar type of errors. I mean my system got collapsed for l-bfgs minimization and for steepest descent the potential energy is a large number.(obviously some bad contacts). It seems the problem is with topology. Earlier I asked about what is meant by broken topology?? Can anyone tell what may ne the problem and also about what is meant by broken topology?? A broken topology is where you haven't managed to describe the bond connectivity in your .top file that you'd like to. The way to fix it is to reduce your problem to its simplest form (single surfactant in vacuum, as David suggests), observe where the breakage occurs, read chapter 5 carefully, and remedy appropriately. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ 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: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Hi Tsjerk and others, I tried to simulate one surfactant and one chloride ion in 500 waters and got similar type of errors. I mean my system got collapsed for l-bfgs minimization and for steepest descent the potential energy is a large number.(obviously some bad contacts). It seems the problem is with topology. Earlier I asked about what is meant by broken topology?? Can anyone tell what may ne the problem and also about what is meant by broken topology?? Thanks and Regards Arun Kumar M.E chem engg Hi Tsjerk and gmx-users, Thank you for the response. And I will be more clear in asking questions. The force field I am using is ffgmx. I am not sure I will obtain good properties for my system with ffgmx at this time. But I want to understand how to set up my simulation which contains ionic surfactants. And yes I will strat it for one surfactant and one counterion in water. In my post, MDRUN means True dynamics( I mean real md not energy minimization). I know that without minimizing the energy it will be bad to do MD. But I just checked how it will work as I kept density around 330 kg/m^3. I think it won't work even. Sorry for confusing with last post. My system's initial configuration is alright it seems(No overlapping atoms and bonds). And after I start EM or MD it's exploding(Why I don't know exactly). Now I will tell the steps I took to start my simulation. Initially I got topology and pdb files(united atom) from PRODRG(gromos 87 force field) for my surfactant behenyl(C22) trimethyl ammonium chloride(charge +1, it won't contain chloride) and stearyl alcohol. And then I got water.pdb,chlorine.pdb from pdb database. I prepared a random configuration of 1400 water molecules, 20 surf, 20 chloride ions and 40 co-surfs in 5X5X8 nm^3 by using packmol. Then I used editconf to get system.gro from system.pdb and also put in a cubic box with this command editconf -f system.pdb -bt cubic -o system.gro But it reported system volume was zero. So I changed end of my .gro file by replacing 0. 0. 0. by 5.000 5.000 8.000. The density is about 330 kg/m^3. So I thought it will be useful in Energy Minimization and also can be adjusted in NPT md simulation. As i have a little experience in DPPC topologies and running simulation for DPPC bilayer phase(successfully) using the files got from Tieleman's website, I prepared a topology file for my system(btm.top). It contains the following lines #include ffgmx.itp #include btm87.itp #include stearyl87.itp #include ions.itp #ifdef FLEX_SPC #include flexspc.itp #else #include spc.itp #endif [ system ] BTM with cosurf [ molecules ] ; name number BTM 20 STR 40 SOL 1400 Cl 20 btm87.itp(surf) and stearyl87.itp(co-surf) are topologies got from PRODRG. I kept all these in my direactory. Now I tried to minmize the energy of the system. First I used grompp to create md input file(I mean for EM). It worked fine. But for mdrun system is exploding(for l-bfgs method). For steepest descent it's not, But the potential energy of the system was a big positive number at end. For my true MD also the system's exploding like l-bfgs minmization after showing that warning earlier I posted. These are the steps I took and results I got. And for last query regarding tc-grps, I coupled the whole system to a heat bath at 300 K. I observed the previous posts. Here with this mail I attached my MD .mdp file. And at last Is there any relation with Mark's(Mark abraham) observations regarding broken topologies in some of the posts I observed, with my problem. Can anyone explain what is meant by a broken topology file. Try to help me to understand these thing well??? I can give any more details if it is needed. Thanks and regards Arun Kumar M.E chem engg Hi Arun, You have to get your methods straight.., and be more clear in the phrasing of your question. I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactant and cosurfactant. What force field do you use? The standard output from PRODRG for gromacs is the gmx force field, which is deprecated and shouldn't be used (this is in the archives). So I minimized the energies for both my molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol. Maybe you're better of trying one surfactant molecule and one chloride in water to start with? I tried to minimize the energy of the system using l-bfgs. But I am always getting the error attached
[gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Dear gmx-users: I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactant and cosurfactant. So I minimized the energies for both my molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol. I tried to minimize the energy of the system using l-bfgs. But I am always getting the error attached below. In my em.mdp file I am using pme for coulomb type. Even for MDRUN also I am getting the same error... I checked the previous posts and I am unable to understand what's the problem. And can anyone tell what is meant by broken topology??? Also try to help me to get out of the problem. Low-Memory BFGS Minimizer: Tolerance (Fmax) = 2.0e+04 Number of steps=1 Warning: 1-4 interaction between 1 and 4 at distance 3.540 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Using 10 BFGS correction steps. F-max = inf on atom 97 F-Norm= nan --- My topology contains a system of four types surfactant, cosurfctant, water and Chloride ions. Until grompp everything is fine. Total charge on system is zero. I can give any more details if it is needed. -- Arun kumar.V M.E Chemical ___ 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: gmx-users Digest, Vol 37, Issue 18
Hi Tsjerk and gmx-users, Thank you for the response. And I will be more clear in asking questions. The force field I am using is ffgmx. I am not sure I will obtain good properties for my system with ffgmx at this time. But I want to understand how to set up my simulation which contains ionic surfactants. And yes I will strat it for one surfactant and one counterion in water. In my post, MDRUN means True dynamics( I mean real md not energy minimization). I know that without minimizing the energy it will be bad to do MD. But I just checked how it will work as I kept density around 330 kg/m^3. I think it won't work even. Sorry for confusing with last post. My system's initial configuration is alright it seems(No overlapping atoms and bonds). And after I start EM or MD it's exploding(Why I don't know exactly). Now I will tell the steps I took to start my simulation. Initially I got topology and pdb files(united atom) from PRODRG(gromos 87 force field) for my surfactant behenyl(C22) trimethyl ammonium chloride(charge +1, it won't contain chloride) and stearyl alcohol. And then I got water.pdb,chlorine.pdb from pdb database. I prepared a random configuration of 1400 water molecules, 20 surf, 20 chloride ions and 40 co-surfs in 5X5X8 nm^3 by using packmol. Then I used editconf to get system.gro from system.pdb and also put in a cubic box with this command editconf -f system.pdb -bt cubic -o system.gro But it reported system volume was zero. So I changed end of my .gro file by replacing 0. 0. 0. by 5.000 5.000 8.000. The density is about 330 kg/m^3. So I thought it will be useful in Energy Minimization and also can be adjusted in NPT md simulation. As i have a little experience in DPPC topologies and running simulation for DPPC bilayer phase(successfully) using the files got from Tieleman's website, I prepared a topology file for my system(btm.top). It contains the following lines #include ffgmx.itp #include btm87.itp #include stearyl87.itp #include ions.itp #ifdef FLEX_SPC #include flexspc.itp #else #include spc.itp #endif [ system ] BTM with cosurf [ molecules ] ; name number BTM 20 STR 40 SOL 1400 Cl 20 btm87.itp(surf) and stearyl87.itp(co-surf) are topologies got from PRODRG. I kept all these in my direactory. Now I tried to minmize the energy of the system. First I used grompp to create md input file(I mean for EM). It worked fine. But for mdrun system is exploding(for l-bfgs method). For steepest descent it's not, But the potential energy of the system was a big positive number at end. For my true MD also the system's exploding like l-bfgs minmization after showing that warning earlier I posted. These are the steps I took and results I got. And for last query regarding tc-grps, I coupled the whole system to a heat bath at 300 K. I observed the previous posts. Here with this mail I attached my MD .mdp file. And at last Is there any relation with Mark's(Mark abraham) observations regarding broken topologies in some of the posts I observed, with my problem. Can anyone explain what is meant by a broken topology file. Try to help me to understand these thing well??? I can give any more details if it is needed. Thanks and regards Arun Kumar M.E chem engg Hi Arun, You have to get your methods straight.., and be more clear in the phrasing of your question. I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactant and cosurfactant. What force field do you use? The standard output from PRODRG for gromacs is the gmx force field, which is deprecated and shouldn't be used (this is in the archives). So I minimized the energies for both my molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol. Maybe you're better of trying one surfactant molecule and one chloride in water to start with? I tried to minimize the energy of the system using l-bfgs. But I am always getting the error attached below. In my em.mdp file I am using pme for coulomb type. Even for MDRUN also I am getting the same error... I checked the previous posts and I am unable to understand what's the problem. And can anyone tell what is meant by broken topology??? Also try to help me to get out of the problem. Even for MDRUN? pfff, that must be really bad then. First of all, do you mean running the program 'mdrun' with the .tpr file for l-bfgs EM, or an actual MD run? In case of the latter, wouldn't you think there's little point in starting an MD run if energy
[gmx-users] problem regarding editconf - atommass
Hai all I am trying to simulate the bulk phase decane system using GROMACS... I used decane pdb file which I goT from HIC UP I changed the residue name to C10 from D10 to match the residue name in ffgmx.rtp(GROMACS force field) I ran pdb2gmx , selected forcefield 4(ffgmx)... and got .top and gro files for my decane molecule...There saw the molecule mass as 142.17 which is correct ... Now as I want to simulate Bulk I used genconf to get my 512 molecule system. i got out.gro file from this. To get the desired density I used editconf to get 602 gr/ltr But here in out put as shown below its showing the different mass for 512 molecules i.e 61498.9.(see output of editconf)..which means that single molecule mass is 120.11...means hydrogen masses are missing... I checked atommass.datand I am unable to know what I have to do. Awaiting for help Arun GENCONF output [EMAIL PROTECTED] ~]$ !genconf genconf -nbox 8 8 8 -dist 1 1 1 -f conf.gro :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. 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. :-) genconf (-: Option Filename Type Description -f conf.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -oout.gro Output Generic structure: gro g96 pdb xml -trj traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb 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 0 Set the nicelevel -nbox vector 8 8 8 Number of boxes -dist vector 1 1 1 Distance between boxes -seedint 0 Random generator seed, if 0 generated from the time -[no]rot bool no Randomly rotate conformations -[no]shuffle bool no Random shuffling of molecules -[no]sort bool no Sort molecules on X coord -blockint 1 Divide the box in blocks on this number of cpus -nmolatint 3 Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system! -maxrot vector 90 90 90 Maximum random rotation -[no]renumber bool no Renumber residues gcq#77: One Cross Each (Monty Python) ### After then I ran editconf to change density .. I used 512 decane molecules... But I did not get the total mass of 512*142=72704 amu... Instead I got 61498.9 which is 512*120 that means hydrogen masses are missing Can anyone help me in this regard. ## Here is the output [EMAIL PROTECTED] ~]$ editconf -density 602 -f out.gro :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. 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. :-) editconf (-: Option Filename Type Description -fout.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -oout.gro Output Generic structure: gro g96 pdb xml -bf bfact.dat Input, Opt. Generic data file Option Type Value Description -- -[no]h bool
[gmx-users] Regarding preparation of .itp file for a new molecule
Hai all... I am a newbie to gromacs simulation software and its file formats. I want to develop coarse grain models for surfactant systems by using atomistic simulations. I got a .pdb file for BTMAC surfactant. But to run simuations on gromacs,I need to include .itp file in source code. Can anyone of u tell me,Is it difficult to prepare a .itp file for a new molecule?? If it is so, I want to know how many days it will take to prepare... And also Please tell suggestions to prepare a .itp file for a new molecule Thanks in advance-- Arun kumar.VM.E Chemical Engg ___ 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
