[gmx-users] Script for detecting interfaces
A couple of months ago someone mentioned a recent publication that went through a procedure for the detection of an interface / surface between phases for data from MD. Remember reading the publication and thinking was pretty neat and need to come back and try it. Well, for the life of me can't find it now, through my links, publication database, googling, literature search etc. Does anyone recall what it was or where I can find it? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] git
Shouldn't you just do it anonymously? git clone git://git.gromacs.org/gromacs.git Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja Sent: Friday, 18 June 2010 3:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] git Thanks Justin. I installed git first and then used git clone g...@git.gromacs.org:gromacs.git and this is what I get Initialized empty Git repository in /fs/home/sm868/gromacs/.git/ The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be established. RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to the list of known hosts. g...@git.gromacs.org's password: 1) Empty repository - what does that mean? 2) What password do I need to enter here? Pooja On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Have you actually installed git? If so, it may just not be in your $PATH. If not, install it before you try to use it :) -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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] FEP for amino acid mutations.
I would make a new residue in the .rtp file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Matteo De Chiara Sent: Monday, 14 June 2010 8:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] FEP for amino acid mutations. Dear GROMACS users, I would like to perform a FEP calculation mutating a residue outside the active site of a protein. I was wondering if I have to create a .itp file for the mutation or it is possible to modify the .rtp file ( adding the state B parameter to the amino acid I would like to change). Of course, in this case, I will create a new amino acid type identical to the one I would like to mutate in order to act only on the amino acid in a specific position. Thanks for your help! matteo -- Ph.D. Student Matteo De Chiara Dept. of Molecular Biology, University of Siena Via Fiorentina 1, 53100 Siena Italy -- 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 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] the box lengths
Please copy and paste in the commands you are using, and the output. I suspect you have made your box bigger, but it still contains the same number of molecules and you still have pressure coupling on. So when you start the simulation, not surprising that the box compresses again and goes under 2nm again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:04 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. Well, what are your box vectors? If they are 2 nm, you will get this error because of the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi on -Justin system size : 4.581 2.380 2.715 (nm) diameter: 4.889 (nm) center : -0.012 0.003 -0.904 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 9.678 9.664 5.461 (nm) new center : 9.667 9.667 4.557 (nm) new box vectors : 12.889 12.889 12.889 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1514.05 (nm^3) This one I set was really large, but still showed that problems. What problems? The same error about the box lengths being shorter than twice the cutoff? I don't think that's possible, given those vectors, if you're keeping your cutoffs at 1.0 nm. -Justin I do keep the cut-off. That's I do not know why. Four times had been tried. Thanks, lina -- 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 -- 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 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] the box lengths
As already mentioned by Justin, unless you copy and paste the commands and output you got, for us to see, we can only have stabs in the dark (which is what I did since you are missing lots of information on what you are actually doing) to what is actually going on. And don't type in the commands into your email client, physically go and copy and paste the text in, otherwise you are filtering it through your own mind. Go and run the series of commands that work, copy / paste the results for us to see. Then go and run the series of commands that don't work, copy / paste again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:32 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths I used the same commands trying another proteins, but no problems. So it's not the reason about the commands I used. It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just the steps I did the energy minimization after ions (NA+ and CL-) added. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 6:48 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Please copy and paste in the commands you are using, and the output. I suspect you have made your box bigger, but it still contains the same number of molecules and you still have pressure coupling on. So when you start the simulation, not surprising that the box compresses again and goes under 2nm again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:04 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. Well, what are your box vectors? If they are 2 nm, you will get this error because of the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi on -Justin system size : 4.581 2.380 2.715 (nm) diameter: 4.889 (nm) center : -0.012 0.003 -0.904 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 9.678 9.664 5.461 (nm) new center : 9.667 9.667 4.557 (nm) new box vectors : 12.889 12.889 12.889 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1514.05 (nm^3) This one I set was really large, but still showed that problems. What problems? The same error about the box lengths being shorter than twice the cutoff? I don't think that's possible, given those vectors, if you're keeping your cutoffs at 1.0 nm. -Justin I do keep the cut-off. That's I do not know why. Four times had been tried. Thanks, lina
RE: [gmx-users] the box lengths
What is the contents of the CRYST1 line in the file try2-water-ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] the box lengths
Well, there's ya problem :-) That specifies the box dimensions. Have a look at try2-water.pdb as well, then you should be able to pin down where the issue has arisen. Appears that one of those steps have failed to write the box dimensions. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 3:37 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths There is none CRYST1 line in the file try2-water-ions.pdb. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:24 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths What is the contents of the CRYST1 line in the file try2-water- ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 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 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] RE: [gmx-user]Error by pdb2gmx (Dallas
I think Dallas might have been thinking of a different file; function types are not required in individual .rtp entries, but you do have to have a proper [bondedtypes] directive at the top of your .rtp file. A few other comments: Yes, sorry. In my case I define the type in the various bond sections within the .rtp file for house-keeping reasons, and isn't actually required. Saw that missing in yours and though that was an issue. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] [gmx-user]Error by pdb2gmx
You have no function types defined in your bonds, angles and dihedrals. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of ??? Sent: Friday, 28 May 2010 11:58 AM To: gmx-users@gromacs.org Subject: [gmx-users] [gmx-user]Error by pdb2gmx Dear Editors: I used gromacs version 4.0.7. I update ffG45a3.rtp to include my molecule with its rtp in the attached file DRG.txt.And the pdb file of my molecule is mol.txt and also attached. When I used the following command,there is an error! pdb2gmx_mpi -ff G45a3 -f iso-C16.PDB Opening library file ffG45a3.rtp Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/gromacs4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /home/gromacs4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /home/gromacs4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /home/gromacs4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /home/gromacs4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading iso-C16.PDB... Read 81 atoms Opening library file /home/gromacs4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 81 atoms chain #res #atoms 1 ' ' 1 81 All occupancies are one Opening library file /home/gromacs4/share/gromacs/top/ffG45a3.atp Atomtype 1 Reading residue database... (ffG45a3) Opening library file ffG45a3.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 96 --- Program pdb2gmx_mpi, VERSION 4.0.7 Source code file: resall.c, line: 344 Fatal error: in .rtp file in residue DRG at line: What's up with the resall.c in line 344? I hope the problem won't bother you too much! Thank you very much! Angel -- 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] polymer simulation
If you are referring to something that will generate a coordinate file (.pdb or .gro) of polymer molecules randomly distributed, then there is not currently a script with GROMACS that will do that job. If you have a single molecule, there are a couple of tools that can randomly spread those molecules around, though not very well. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] enegry minimisation
I seem to say this several times per week: in my experience (and in the experience of many others who have posted here) the charges and charge groups output by PRODRG are often unsatisfactory, requiring manual Might be an idea then to put the comments on the PRODRG page on the GROMACS website / wiki and direct people there? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] g_sdf : error
g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- 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 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] g_sdf : error
Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- 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 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 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 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] g_sdf : error
As I suspected: Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements As the error has told you, C3 does not have the same number of elements as C2 and C4. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 11:21 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error Here are details. the first three groups from GUL residue and the last in cation (residue) Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements Group19 ( C5) has 1 elements Group20 ( C6) has 129 elements -- -- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements - - Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements Select a group: 16 Selected 16: 'C2' Select a group: 17 Selected 17: 'C3' Select a group: 18 Selected 18: 'C4' Select a group: 39 Selected 39: 'EMI' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 --- Program g_sdf, VERSION 4.0.5 Source code file: gmx_sdf.c, line: 177 Fatal error: For single particle SDF, all reference groupsmust have the same size. --- Nilesh On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote: Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting
RE: [gmx-users] non zero charge in topolgy
You can call the following whatever you want to: [ moleculetype ] ; Namenrexcl Protein 3 This would probably be more appropriate: [ moleculetype ] ; Namenrexcl Hexane 3 And this section, doesn't really matter what it says here either, this part is really for your own information: [ system ] ; Name Protein This would probably be more appropriate: [ system ] ; Name Single hexane molecule And finally this bit has too, of course, match with what moleculetype you have defined: [ molecules ] ; Compound#mols Protein 1 So if you did the above, you would change this to: [ molecules ] ; Compound#mols Hexane 1 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] grompp, energy minimization,, output file error
For starters there is no residue name in your .gro file, you simply have a number. First column should be … 1HEX C1 1HEX C2 . . . 1HEX H14 2HEX C1 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] warning when process the files with grompp
It is most likely due to having the order of your molecules in the topology file (.top) different to those that are in coordinate file (.gro). Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of kecy...@sina.com Sent: Thursday, 22 April 2010 1:14 PM To: gmx-users@gromacs.org Subject: [gmx-users] warning when process the files with grompp Hello, I want to generate the em.tpr file, but it arise the warning like this : Warning: atom name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW) Warning: atom name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1) Warning: atom name 3 in TBP_wat.top and 10tbpc12wat1.gro does not match (C7 - HW2) Warning: atom name 4 in TBP_wat.top and 10tbpc12wat1.gro does not match (C6 - OW) Warning: atom name 5 in TBP_wat.top and 10tbpc12wat1.gro does not match (O5 - HW1) Warning: atom name 6 in TBP_wat.top and 10tbpc12wat1.gro does not match (P1 - HW2) Warning: atom name 7 in TBP_wat.top and 10tbpc12wat1.gro does not match (O4 - OW) My system is water and dodecane (from 0 to 5 nm of the z axis is water box, 5 to 10 nm dodecane box), and the TBP dissolves in the dodecane, if I overlook it , mdrun can not do the energy minimization well, and the TBP molecule will be tattered. I hope you can help me ,thank you very much! -- 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] help
See section 5.7.1 of the manual , it shows you exactly how you define angles, bond, dihedrals etc for any type of molecule in the topology files for GROMACS. If after the theory, see section 4.2 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of udaya dahal Sent: Tuesday, 20 April 2010 10:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] help Respected Sir/Madam, I am student of Tribhuwan University and trying to find out diffusion coefficient of D2O in H2O. But due to lack of access of journal i am not being able to complete my job. Can any tell me how to define angle in the topology file and the value of harmonic constant of D2O. I am really in very serious trouble. Udaya Raj Dahal Tribhuwan University Nepal Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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] Lateral pressure profile in membrane simulations
Isn't that already present in the energy file, .edr, from the run? Simply use g_energy to extract it. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Fernando E. Herrera Sent: Thursday, 8 April 2010 8:45 AM To: gmx-users@gromacs.org Subject: [gmx-users] Lateral pressure profile in membrane simulations Dear users: I am doing some molecular dynamics simulations of membrane systems and i would like to ask you if someone know or have a code for the calculation of the lateral pressure profile from the data obtained doing membrane simulations. Thank you very much in advance, Fernando -- 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] energy minimization in charged systems
What are the atoms that are causing the problems actually doing, where are they located etc? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Bhadauria Sent: Thursday, 8 April 2010 3:11 PM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization in charged systems Hi all, I am trying to simulate a electroosmotic flow in a nanochannel. System consists of water + (Cl-) ions in a channel confined of silicon 111 walls. I start with taking water as only solvent, equilibrating the system for about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-) ions. Walls are charged appropriately to maintain electro-neutrality in the system. The problem is with Energy minimization after inserting ions using steep algorithm (haven't turned on the electric field yet). I am getting an error like this: t = 0.038 ps: Water molecule starting at atom 2569 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates and Steepest Descents converged to machine precision in 88 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.75456106043895e+06 Maximum force = 1.07111309902475e+11 on atom 4898 Norm of force = 1.48772609239112e+09 If it were only couple of such molecules, I could have removed them easily from the gro file. The problem is twofold, there are around 10 molecules which give this error message, plus even after removal of these molecules, energy minimization results in the same error on different sets of molecules. I have tried a number of ways to tackle this including tuning the time step. Is there any way to avoid this? Any help would be appreciated. Thanks in advance. -- Ravi Bhadauria -- 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] about water models
Probably already seen it, or beyond it now, but a good primer is http://www1.lsbu.ac.uk/water/models.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] density vs time
g_energy Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of nishap.pa...@utoronto.ca Sent: Wednesday, 17 March 2010 8:32 AM To: gmx-users@gromacs.org Subject: [gmx-users] density vs time Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tried using g_density but it gives me density vs box(nm). Any suggestions would be useful. Thanks. Nisha P -- 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 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] rdf problem
If you have aggregation and a small box size, then the rdf will not be able to asymptote to one. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Antonia V. Sent: Thursday, 11 March 2010 2:18 AM To: gmx-users@gromacs.org Subject: [gmx-users] rdf problem Dear all, I am simulating a binary system of two non mixing components (5CB and water using version 4-0-3; the whole equilibrated trajectory is about 300ns). I want to calculate the rdf of the centers of mass of 5CB using the command g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr. The problem is that the rdf I am getting does not approach one at long distances. Is there a way to correct that? I have the same problem, with all rdfs, and also when I compute the rdfs for a lipid bilayer (DPPC-water)... I think it has to do with the way that the normalization is done, because the ones that are calculated for a one component system (i.e. bulk 5CB) are normal (they do approach one). Thank you, Antonia Hotmail: Trusted email with Microsoft's powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 Hotmail: Powerful Free email with security by Microsoft. Get it now. https://signup.live.com/signup.aspx?id=60969 -- 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] large number of molecules
You are going to have to provide a lot more details than that if you want some help. What is wrong results? What is your input (copy and paste some commands in)? What is the output (copy and paste)? What makes you think the results are wrong? In what situations are they right? ... and there are a lot more questions that could be asked .. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of ksm tprk Sent: Tuesday, 9 March 2010 8:33 AM To: gromacs users Subject: [gmx-users] large number of molecules Hello, I simulate carbon nanotube and basically I follow up http://cs86.com/CNSE/SWNT.htm But when I increase the number of molecules (like 15000) , it gives me wrong results. Do you know why this is happen? Thank you, Kasim Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. http://clk.atdmt.com/GBL/go/201469229/direct/01/ -- 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] ethanol bond types
Thanks David. These are the parameters I added. Do you think they seem reasonable? You might as well run a simulation yourself, it will be quickly apparent if something is very wrong. Best way to determine these things is try it and see for yourself. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] Anisotropic pressure control
Why is it that what you have run with xy rigid and z couple not correct? Fluctuating box volume is exactly what you would expect to get, and do get, with pressure coupling. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Matteus Lindgren Sent: Friday, 26 February 2010 8:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] Anisotropic pressure control Dear experts, I am trying to run MD on a protein in water above a flat surface of TiO2 in a cubic box with pressure control. All the atoms of TiO2 are frozen and I therefore think that anisotropic pressure control must be used. I tried allowing box fluctuations in the direction of the normal vector (the z-axis) of the TiO2 surface but the box volume then oscillates during the whole simulation. The same parameters worked for a simulation of protein+water without the frozen TiO2 surface. How can I use pressure control for a system with a frozen surface that extends through the whole box? Ive read the posts about membrane simulations but membranes are flexible so I think those suggestions might not apply. The important part of the input file was as follows: nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.2 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1.5 energygrp_table = fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes Tcoupl = Nose-hoover tc-grps = protres RUT solcl tau_t= 0.1 0.1 0.1 ref_t= 310 310 310 Pcoupl = Parrinello-Rahman Pcoupltype = anisotropic tau_p= 2.0 2.0 2.0 2.0 2.0 2.0 compressibility = 0.0 0.0 5e-5 0.0 0.0 0.0 ref_p= 0 0 1.01325 0 0 0 gen_vel = yes gen_temp = 310 gen_seed = 1993 constraints = hbonds constraint-algorithm = lincs continuation = yes lincs-order = 4 lincs-iter = 4 freezegrps = frozen freezedim= Y Y Y Thanks Matteus - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 -- 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] energy minimization problem
Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of sarbani chattopadhyay Sent: Friday, 26 February 2010 12:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization problem Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able to get the Fmax below e-02. i have tried using the l-bgs minimization technique. The lbfgs.mdp file is as follows define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit = 0 nsteps = 1 nbfgscorr = 10 emtol = .001 emstep = 0.5 gen_vel = no gen-temp = 300 nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = no Pcoupl = no coulombtype = PME vdwtype = shift The minimization continues up to the specified no. of steps. When I try to give another minimization run on the minimized structure, the Fmax goes upto the order e+00. I am not being able to figure out the problem. Any suggestion regarding this will be very helpful. Thanks in advance Sarbani. http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? ~WRD000.jpg-- 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] Assembling a good simulation starting point
Can you run that same procedure without doing anything to your protein? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of John Ladasky Sent: Friday, 19 February 2010 2:08 PM To: gmx-users@gromacs.org Subject: [gmx-users] Assembling a good simulation starting point Hello everyone, I'm a fairly new GROMACS user. I'm running GROMACS 4.0.5 on top of Ubuntu Linux 9.10. I am still learning a lot. I just tried to set up my first fairly complex simulation, and it failed. I have a protein of interest, a beta barrel with a hydrophobic, ligand-binding interior. I am interested in making mutations to this protein, with the goal of getting it to bind to a rather different ligand than the one it normally binds. The way that I propose to go about studying this problem is to construct a partially-unfolded version of the protein structure, add my ligand of interest, and then run an energy minimization. My first naive attempt to construct the partially-unfolded protein was not successful. I knew that it might have problems, but I tried it anyway. Using Biopython, I rotated the atomic coordinates so that the beta barrel was parallel to an axis. Then I simply pulled all of the atoms 3 Angstroms away from the axis. Finally, I inserted my ligand. Visually, inspecting the starting structure with PyMol, I didn't see anything egregious. However, I could have some unwanted close contacts. I got a few long bond warnings from pdb2gmx, but I persisted. I got through genbox, editconf, and my first grompp sucessfully. But then when I tried the first, position-restrained energy minimization, it aborted with too many LINCS warnings. I blew the system up. These LINCS warnings could come from close contacts, or from large forces in over-stretched bonds which resulted from my crude approach to expanding the protein structure. Whatever the cause, I need a smarter way to start. I am open to ANY suggestions! What I THINK I might want to do is to manipulate the starting structure in a more natural way. For example, selecting some peptide bonds in the beta turns, and changing their angles. A program which allows me to manipulate structures, and not just simulate natural forces, is what I think I need. Surely, people who have used GROMACS will have faced problems simliar to mine. Thanks for your advice! John Ladasky -- 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] rdf
A single methane molecule in water, it is not surprising at all that there is some noise in the rdf produced. If you want it smoother than that, you will simply having to run it for longer. The rdf is an average, insufficient data points mean it will be noisy, you cannot get around that fact. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of nishap.pa...@utoronto.ca Sent: Monday, 1 February 2010 9:57 AM To: gmx-users@gromacs.org Subject: Re: [gmx-users] rdf Hi, I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3 3 3 (nm). My topology file is : ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Methane3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_138 1 METH C 1 -0.24 12.011 ; qtot -0.24 2 opls_140 1 METH H1 1 0.06 1.008 ; qtot -0.18 3 opls_140 1 METH H2 1 0.06 1.008 ; qtot -0.12 4 opls_140 1 METH H3 1 0.06 1.008 ; qtot -0.06 5 opls_140 1 METH H4 1 0.06 1.008 ; qtot 0.54 [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 ; Include water topology #include tip3p.itp [ system ] ; Name methane pair in water [ molecules ] ; Compound#mols Methane 1 SOL 893 and my grompp file at constant volume is: ; VARIOUS PREPROCESSING OPTIONS title= Methane in water cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 5000 comm_mode= Linear nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1000 nstenergy= 1 nstxtcout= 1000 xtc_precision= 1000 xtc-grps = System energygrps = nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.4 coulombtype = pme rcoulomb = 1.4 epsilon_rf = 1 epsilon_r= 1 vdw-type = cut-off rvdw = 1.4 Tcoupl = V-rescale tc-grps = System tau_t= 1.0 ref_t= 298 Pcoupl = No Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 2 lincs-warnangle = 30 Does this makes sense? And Chris, I don't understand what you mean by defining tail of my rdf. -Nisha Quoting chris.ne...@utoronto.ca: make a figure of your rdf, post it online somewhere (I use photobucket) and reply to the list with a link to your figure. Make sure your figure is well labeled and give us a thorough description of what you see that you don't like. Also tell us what your unit-cell box vectors are. Also describe your system thoroughly, e.g. one methane in a box of 100 water molecules... I know that the meaning of values fluctuate alot (i.e. decreasing). is immediately obvious to you, but for those of us who haven't seen the graph it is pretty tough to figure out what is actually going on. And off the bat, I'd say that the tail of your RDF is just poorly defined (data coming from few waters in the figurative corners of the unit cell for a central methane) and you are seeing the noise that results from this -- Try regenerating your data by block averaging into 0-33 ns, 33-66
RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial
So, what EXACTLY are you doing? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of vivek sharma Sent: Monday, 25 January 2010 7:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand is away from the molecule after editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek 2010/1/25 Tsjerk Wassenaar tsje...@gmail.com Hi Vivek, Now when I am processing the modified .gro file to generate box, the ligand and cofactor are going away from the protein molecule and I am not able to analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 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] checkpoint MDRUN -cpt question
Have a read of http://www.gromacs.org/Documentation/How-tos/Extending_Simulations in particular the section down the bottom that is appropriate for the version of GROMACS you are using. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Miguel Quiliano Meza Sent: Friday, 22 January 2010 9:14 AM To: gmx-users@gromacs.org Subject: [gmx-users] checkpoint MDRUN -cpt question Hi everyone. I am a relative new user of GROMACS. I have performed some short simulations but now I want to something big. I have been reading on the web site and found that mdrun -.cpt option is used to generate checkpoints, I am using GROMACS 3.3.3 but I don't find -cpt option when I call mdrun -h I would very grateful if someone can help me with how to do a checkpoint with GROMACS 3.3.3? Best Regards. -- 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] atomnumber=-12345
Might be a good idea to provide the input and output that generated the
error.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Itamar Kass
Sent: Thursday, 21 January 2010 11:13 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] atomnumber=-12345
Hi,
After one of my simulation had crashed, I had used gmxdump to look into
it. What stoke me was the all atoms have the same atomnumer:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01, q=
1.29000e-01, mB= 1.40067e+01, qB= 1.29000e-01, resnr=0,
atomnumber=-12345}
atom[ 1]={type= 1, typeB= 1, ptype=Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
atom[ 2]={type= 1, typeB= 1, ptype=Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
atom[ 3]={type= 1, typeB= 1, ptype=Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
atom[ 4]={type= 2, typeB= 2, ptype=Atom, m=
1.30190e+01, q= 1.27000e-01, mB= 1.30190e+01, qB= 1.27000e-01, resnr=
0, atomnumber=-12345}
and so on...
I wonder if someone knows what the origin of this error and how to over
come it?
In addition, it is vary strange that the simulation run for 100ps before
it crashed.
All the best,
Itamar.
--
In theory, there is no difference between theory and practice. But, in
practice, there is. - Jan L.A. van de Snepscheut
===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au
--
gmx-users mailing listgmx-users@gromacs.org
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RE: [gmx-users] Fwd: What could be wrong with rdf plot?
Wouldn't it be simpler to just exclude the intramolecular -OHs when you actually generate the RDF? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of XAvier Periole Sent: Tue 1/5/2010 6:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot? It is always better to keep the discussion in the list. Someone could benefit of it as well as you from others. From: Lum Nforbi lumngwe...@gmail.com Date: January 4, 2010 7:57:04 PM GMT+01:00 To: XAvier Periole x.peri...@rug.nl Subject: Thank you for reply on RDF PLOT problem/Question. Hi Xavier, Is there something I can do in order to eliminate this peak, maybe like making adjustments to my coordinate file? In your coordinates no, but you can just erase it. I am not actually sure of how the normalization of the rdf is done considering that this pick should not appear in the analyses! Either someone else knows or you have to find out our self, looking at the code or in the archive :)) Thank you, Lum Message: 3 Date: Sun, 3 Jan 2010 13:18:29 +0100 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 28fdb30b-7b96-4975-bd1d-d6120f1b4...@rug.nl Content-Type: text/plain; charset=us-ascii I am not sure somebody gave you an answer ... the first intense and probably very narrow pick is very likely due to the intramolecular OH distance. It should be around 0.1 nm, isn't it? On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote: -- Forwarded message -- From: Lum Nforbi lumngwe...@gmail.com Date: Thu, Dec 31, 2009 at 12:33 PM Subject: What could be wrong with rdf plot? To: gmx-users@gromacs.org Dear all, I am currently analyzing a system of 2000 molecules of TIP3P water on which I performed a NPT simulation. The plot for g(OO) looks very good but for some reason unknown to me, on the g(OH) plot there is an intense peak coming before the normal peaks that are characteristic of a g(OH) plot. Could someone tell me what is going on? I have attached the graphs for gOO and gOH for viewing. Also, I have still not been able to figure out how to calculate the Cp of my system and I have been struggling with this for over a month now. g_energy for my system gives a wrong Cv (~12). Can someone explain to me or give me hints on how to calculate the Cp of an NPT simulation of TIP3P water, please? Have a wonderful New Year 2010 and Decade (2010-2019)! Thank you, Lum RDF_OWHW1HW2_0_8000PS-- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100103/ef8a/attachment-0001.html winmail.dat-- 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] g_sdf and visualizing using gOpenMol
Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf). Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check if there is a bug submitted for it. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Jennifer Williams Sent: Tue 12/15/2009 11:41 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot contourimport) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught = : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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 winmail.dat-- 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] g_sdf and visualizing using gOpenMol
Also, forgot to mention, if you use VMD, it will load it as well. With VMD you don't need any structure file to load the .plt file, just load it as a new molecule. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Dallas B. Warren Sent: Wed 12/16/2009 8:25 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf and visualizing using gOpenMol Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf). Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check if there is a bug submitted for it. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Jennifer Williams Sent: Tue 12/15/2009 11:41 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot contourimport) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught = : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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 winmail.dat-- 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] g_sdf and visualizing using gOpenMol
FYI, there is a listing in bugzilla http://bugzilla.gromacs.org/show_bug.cgi?id=356 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat-- 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] fftw vs cmkl
3D-FFT under both situations is 21.4% and PME mesh down as 54% (figures taken from the second last and last tables in the .log file, respectively). Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 12/11/2009 11:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fftw vs cmkl Dallas B. Warren wrote: Thanks Mark. My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps fftw 3.2.1 - 20,027 seconds Intel cmkl - 19,792 seconds So about 1.2% faster. IIRC icc does a better job on mkl than gcc. Of course you need to make sure the PME job is being dominated by the FFT part to be sure you're measuring a relevant speed difference. The output at the end of the log file reveals this. Mark -- 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 winmail.dat-- 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] splitting a trajectory
Another option is to create a new trajectory file to use in your analysis, using trjconv Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 12/11/2009 3:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] splitting a trajectory Ramachandran G wrote: Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the trajectory file. Thanks for your help Make use of the -b and -e flags, which should be present in all of the analysis tools. -Justin Rama -- 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 winmail.dat-- 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] fftw vs cmkl
Just wondering if anyone has done a comparison of GROMACS complied using fftw versus cmkl? SC tech suggested that cmkl might be a bit faster, but can't find any mention of someone making a comparison between them anywhere, searching users list and web for cmkl (is there may be another term used for it?). Are running a test myself to see, so will report back with that once it is done. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat-- 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] Re:Re: g_helixorient problem
Command lines that you use? Contents of the index files? Contents of the output files? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of stefhoor Sent: Wed 12/9/2009 1:44 AM To: gmx-users@gromacs.org Subject: [gmx-users] Re:Re: g_helixorient problem Stefan Hoorman wrote: I am trying to analyse the tilt of my helix with g_helixorient, but all analysis come back as a straight line in 0. I have supplied g_helixorient with the index file containing all carbon alpha atoms of a single helix but simply cannot obtain anything more than this zero line graphic. Some help on the matter would be great. Something's wrong, but we can't possibly tell what without a lot more information. Mark Ok then. My system comprises of a helix of 30 residues inserted into a membrane model DPPC. The protein was inserted aligned to the z axis, which is the normal axis of the membrane. The simulation was carried out for 50ns and the hole system is properly equilibrated. From visual inspection, it is possible to see that the helix is tilted compared to the normal axis. For the g_helixorient analysis, I have created an index file containing all the alpha carbon atoms that constituted my helical domain and analysed the hole trajectory with g_helixorient. The tilt.xvg and also the other outputs all come out as a straight line parallel to x, and 0 in the y axis. If there is any more information please tell me if you need any more information. Thank you winmail.dat-- 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] spatial distribution function (SDF)
First three groups are the reference group, from which the SDF is generated, it sets the coordinate system. That means you need to have at least three atoms in the molecule you are generating the SDF from. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of naimah haron naimah Sent: Thu 12/3/2009 9:03 PM To: gromacs Subject: [gmx-users] spatial distribution function (SDF) Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA winmail.dat-- 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] Unexpected behavior of g_msd
trjconv Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Darrell Koskinen Sent: Thursday, 26 November 2009 12:48 PM To: gmx-users@gromacs.org Subject: [gmx-users] Unexpected behavior of g_msd Hi Tsjerk, I looked at the .trr file and cannot read this file and simply delete lines to create a sub-trajectory. So, how do I create a sub-trajectory to analyze? Thanks. Darrell Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Unexpected behavior of g_msd To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff898150911250004l42fee014qf3298816c9ef3...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, You can check whether the output is identical to a trajectory of the specified frames... It may well be that the counting for the regression is done on the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the code... But using a subtrajectory may give you good hint. Hope it helps, Tsjerk On Wed, Nov 25, 2009 at 7:42 AM, Darrell Koskinen darre...@ece.ubc.ca wrote: Dear GROMACS-ites, I am a little confused by the behavior of g_msd. I have a trr file with data points from t=0 to t=100 ps and thought that the following command would perform a regression for the data points between t=60 ps and t=100 ps to determine the diffision constant of the ammonia gas in the simualtion: *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100* However, the output: * /trn version: GMX_trn_file (single precision) Reading frame 900 time 90.000 Used 4 restart points spaced 10 ps over 39.9 ps Fitting from 4 to 35.9 ps D[ NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm2/s /* seems to indicate that the regression was performed between t=4 ps and t=35.9 ps. Could you please explain to me what is happening? Thanks. Darrell -- 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 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] Hydrated radius of ions
That depends on what you are interested in. The radius of all of the ions or a single ion? (if the latter, you will need a long simulation to get enough statistics to make it half decent). Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Manik Mayur Sent: Saturday, 21 November 2009 1:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Hydrated radius of ions 2009/11/20 Dallas B. Warren dallas.war...@pharm.monash.edu.au g_rdf ? Thanks, but while using g_rdf, when I have lots of ions, do I have to make an ndx file entry of a single ion or I have to supply the whole ion group while selecting the reference group. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Manik Mayur Sent: Friday, 20 November 2009 2:10 AM To: Discussion list for GROMACS users Subject: [gmx-users] Hydrated radius of ions Hi, Is there any gromacs utility to calculate the hydrated radius of ions? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA -- 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 Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA -- 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] Hydrated radius of ions
g_rdf ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Manik Mayur Sent: Friday, 20 November 2009 2:10 AM To: Discussion list for GROMACS users Subject: [gmx-users] Hydrated radius of ions Hi, Is there any gromacs utility to calculate the hydrated radius of ions? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA -- 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] How to check for bad contacts
When you try to minimise, it will typically tell you the worst offending atoms in your system. Which you can then check visually using VMD etc and try and work out why it is an issue. Then you can adjust how the system was set up to fix the issue. Also, if you just look at the system visually (though can be an issue with larger systems) if there is something that is really out of place, it can be easy to spot. Such as two molecules too close, interlocked, or severely distorted. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Lum Nforbi Sent: Friday, 20 November 2009 9:19 AM To: gmx-users@gromacs.org Subject: [gmx-users] How to check for bad contacts Hello, How do you check for bad contacts in a system that cannot be minimized? Thanks, Lum -- 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] User results for another run
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Jack Shultz Sent: Friday, 20 November 2009 9:56 AM To: Discussion list for GROMACS users Subject: [gmx-users] User results for another run I must have asked this before but I'm trying find the answer again. If I want to use the results from mdrun for another run following the first time interval, what do I need to do? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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 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] Docking with PyMol and using Gromacs
Coordinate files like pdb and gro aren't used by GROMACS to provide any bonding information. That is what the topology files are for. So their presence in your pdb isn't an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren't actually there at all in the pdb file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Gunnar Widtfeldt Reginsson Sent: Thursday, 12 November 2009 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- 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] some prolem about genbox genconf and editconf
How are you visualizing the system? Using VMD? In that case, bonds are determined by how far apart the atoms are, it guesses what the bonding is, since a .gro file (or a pdb) doesn't have any bonding information in it. So what you are seeing is simply the fact you have scaled the box, increasing or decreasing the distance between the atoms. After a quick EM the atoms will return to their correct spacing. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of DreamCatcher Sent: Wednesday, 28 October 2009 1:50 PM To: gmx-users@gromacs.org Subject: [gmx-users] some prolem about genbox genconf and editconf Hi everybody, I have come across some problem when using genbox, genconf and editconf try to make a box with a certain density and a certain number of polymer chains. First, I use genbox to have one polymer chain filled in the box without any solvent.Then I use genconf to pile up 27 polymer chains ,after that I use editconf to designate a density of 0.3 g/ml to attain the final goal. When I finish it, i find that all the bond that connect the atoms are gone and all the atoms disperse in the box. In another try, I first use a pdb file which contains only one polymer chain to genconf a box with 27polymer chain, and then use editconf to designate the density, but finally I get a box with lots of bonds that might not present in a normal structure, like a carbon was bonded with a 3 or 4 or even more atoms distance long and the bonds connect with it is overcount. What is the prolem? How can I fix it? Thanks in advance, Celeste ___ 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] g_rdf and number of atoms to include
Omar's response answered that question on why they are different. In the first one you are grouping all three into one group, second is just one of the hydrogen types. The fact that the rdf you get is different indicates that all three hydrogens are not identical. Have you compared the rdf for each hydrogen type individually? Another factor may also be that in the first you have three times the number of data points, which can smooth out the curves more. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Enemark Soeren Sent: Wednesday, 21 October 2009 8:28 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_rdf and number of atoms to include Hi Omer, Thanks for your input. Let me reformulate my problem: I have glycine molecules in the form of zwitterions: 1ZGLY N1 0.560 0.337 0.388 -0.0759 -0.2488 -0.5471 1ZGLYH12 0.625 0.312 0.461 0.6035 0.5922 -0.4315 1ZGLYH23 0.601 0.311 0.299 0.1500 -0.3357 -1.5372 1ZGLYH34 0.553 0.433 0.388 0.5086 2.8817 -1.8023 1ZGLYCA5 0.426 0.272 0.403 0.3095 0.1790 -0.0455 1ZGLY HA16 0.352 0.335 0.345 -0.9032 0.4782 0.1366 1ZGLY HA27 0.433 0.173 0.358 0.7875 0.5369 -3.0389 1ZGLY C8 0.378 0.267 0.551 0.1816 -0.4672 0.1868 1ZGLY OC19 0.449 0.218 0.644 -0.2820 -0.4080 0.2048 1ZGLY OC2 10 0.263 0.320 0.559 -0.0662 -0.2935 -0.8010 Now, I am interested in the interaction between the amine group hydrogen atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group in an index file: 1. aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine molecules in my system) 2. aOwat (which contains all oxygen atoms in the water molecules in my system) However, I also tried setting up a different index file with the groups: 1. aH1 (which contains all H1 atoms in my system) 2. aOwat (like before) I find that these 2 index files do not produce the same RDFs. Why is that? Best regards, Soren From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch Sent: Wednesday, October 21, 2009 4:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf and number of atoms to include On Wed, Oct 21, 2009 at 07:28, Enemark Soeren ch...@nus.edu.sg wrote: Dear users, I would like to compare interactions between molecules by using RDF. I have tried looking at glycine and water, and compare the following two interactions: 1) between the amine hydrogen atoms in glycine and the oxygen atom in water 2) between the carboxyl oxygen atoms in glycine and the oxygen atom in water However, my result in 1) depends on how many of the 3 hydrogen atoms I include in the calculations. Why is that? If you mean that when focusing your RDF calculations on either one of the three hydrogens results in three different RDFs then it means that each hydrogen feels water differently. I bet this difference is only for the first peak of g(r) and the other peaks overlap between the three RDFs. As for how reasonable this result, its not unlikely because glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H), depending on the protonation state. You might want to provide more details on the system you are studying to get better answer. I am assuming that the RDFs are converged so that including more trajectory data and/or sampled molecules and/or changing bin size does not result in a drastic change to the curves. Does that mean that I cannot directly compare the strengths (RDF peak height) of the two interactions as they are not based on the same number of atoms? Does it also mean that I must always calculate RDFs by using 1 atom on each of the particles/groups that I am comparing? I am not sure how good it is to use the first peak of g(r) to analyze strengths, but you should also consider the width and area under peak. This peak is an average on all nearest neighbours, bonded or not, so it might not give you a good estimate of the hydrogen bond, for example. If you are unsure of your g(r) calc it just for water (that is - only oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should fluctuate around 1. Bests, Omer Markovitch. ___ 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
RE: [gmx-users] Pressure problem: pressure is too large during MDsimulation
Plot the fluctuations of the pressure with time for the simulation. Far better way I think to get an idea of what is going on with a property than just looking at values in a log file. Especially when you are starting out. With pressure coupling, it is not unusual to have a fluctuation of a hundred or so. And that is nothing to worry about, entirely normal behaviour to observe. And with such large fluctuations, the average pressure can deviate from the reference pressure. Of course, with more sample points and longer simulation time, it will get closer to the reference value. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pan Wu Sent: Monday, 12 October 2009 2:20 PM To: gmx-users@gromacs.org Subject: [gmx-users] Pressure problem: pressure is too large during MDsimulation Hi gmx users, I am now simulating one protein with solvent, in all atom forcefield, gromacs official distributed version. The pressure of system seems to be unreasonable large, and during the whole process, the box keeps increasing. Here is how I set up the system, 1. I solvate the proteini use spc216.gro, the log file shows: Output configuration contains 40990 atoms in 12386 residues Volume: 412.593 (nm ^3) Density: 1015.79 g/L Number of SOL molecules: 13410 2. Then I start to do MD with constrains (40 ps), then MD without constrains. The md.log shows pressure keeps decrease, start from 5.79 e+02 until at last to about 3.14e+00, so you can see how large the box size is enlarged. However in my setup, what I use for P-coupling is the same: Pcoupl = Berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 my integral step size is 1fs, so the tau_p = 0.5 ps should be enough. Also I checked the temperature, it is constant during the MD process. (303K) So from these setup process, I think: the density is correct for solvent water and system; the compressibility is chosen as for standard water, the ref_p is chosen as 1.0. Why the pressure is so large? Thank you in advance! -- Sincerely = Pan Wu Graduate Student in Department of Chemistry Duke University 124 Science Drive 5301 French Family Science Center Durham, NC 27708 Phone: (919) 660-1583 = ___ 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] increasing the system size
You don't really need to do anything. Atom number simply starts again. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Amit Choubey Sent: Fri 10/9/2009 9:12 AM To: Discussion list for GROMACS users Subject: [gmx-users] increasing the system size Hi everyone, I was looking for ways to increase the system size (no. of atoms) beyond 9 . I read somewhere that there is no inherent constraint in gromacs on system size rather its because of the format of .gro . I cant find where i read this but could someone suggest me what to do if i need to go beyond 9. thank you, ___ 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 winmail.dat___ 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] Load imbalance and Y size error
No. My system is a single protein with charged ligand associated with it. But why should box size shrink ? In solvated system it does not shrink. What effect vacuum could possibly have on it ? Sounds very much like you have pressure coupling on. Check your .mdp file. Catch ya, Dallas Warren winmail.dat___ 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] Snapshots in different files
If the time frame between snapshots is not too short, you could have that as the length of each MD run, then simple extend the run to keep on going. Could be a bit inefficient. (This is how you should run MD anyway, to ensure don't lose a lot of information if the computer system you are running on crashes etc.) I wouldn't be too surprised if it was possible to hack the code so that a coordinate file is spat out at some interval (even with a limited index of atoms). But that is something for those that know the ins and outs of the code to tell you. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Arik Cohen Sent: Thursday, 8 October 2009 9:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Snapshots in different files Thanks for answering. This would not be the case so much since another program(sniffer) can be working along side gromacs examining each snapshot(Max 400 residues == atoms. I'm only interested in the C-alpha) and then if all criteria are met to extract/or save the coor and if not to erase the snapshot. The aim here is to do an MD from which an ensemble of the C-alpha will be created. Thanks again Arik Mark Abraham wrote: Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. As Justin said, you can't do that. For starters, it consumes vast amounts of disk. Also, it doesn't take long to do it after the fact on some workstation, and it is wasteful to spend your (limited) main compute resources doing I/O while post-processing output. GROMACS workflows are intended to run the simulation fast and efficiently, and then allow you to process the results with the various tools/filters to extract the data you need. You can even post-process with mdrun -rerun if you want to get only a subset of forces or something. The main exception to this principle is the use of xtc-groups, IIRC. Why do you even want separate PDB frames? Visualization tools like VMD will read the trajectory files. Mark ___ 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 No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.421 / Virus Database: 270.14.5/2419 - Release Date: 10/07/09 05:18:00 ___ 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] problems with gromacs preprocessor
Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file by removing the following ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp Since there is no needs also ions.itp , because I didnot add any ions to the structure. Is this right? Not at all, as demonstrated by ... Finally, I tried to use grompp again with the modified topology file. I gety a different error message Fatal error: No such moleculetype SOL I donot know why SOL (water) didnot recognized by grompp !! You removed the .itp that specifies water, spc.itp, so it is not surprising that it no longer knows what SOL is. How can I fix these problems ? Have a look at http://www.gromacs.org/index.php?title=Documentation/Error down the page in the grompp section the original error you came across is dealt with. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] G96 bond, angle and dihedral types for unusual covalent linkages
If there isn't one in the forcefield already, then it is something that you have to parameterise yourself. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of jayalakshmi sridhar Sent: Wed 9/16/2009 4:32 AM To: gmx-users@gromacs.org Subject: [gmx-users] G96 bond, angle and dihedral types for unusual covalent linkages Dear GROMACS Users, I have a protein in which the S-atom of a cysteine residue is bound to the Fe atom of Heme residue by a covalent bond. I need to specify the G96 bond, angle and dihedral types in the .top file. Where can I find this information. Thanks for the help. Jaya. winmail.dat___ 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] how to use a new force field
Best if you don't mess with the ones that are installed. Set up your own forcefield files in a local directory and edit those, GROMACS scripts will then look in the local directory first, before going to the installed one. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Amit Choubey Sent: Wednesday, 9 September 2009 11:53 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] how to use a new force field Hi, so is it a good idea to edit the original gromacs files in top directory for introducing new force field or is there a way to compliment the existing FF files by a new file made by me? Amit On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: hi gromacs user, Is there any good way to introduce new force field in the gromacs library? Read in the manual about the organization of existing force fields, as well as the component files that are necessary to make it function. Beyond that, look at the implemented force fields themselves and see how they work together. -Justin Amit ___ gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 list gmx-us...@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 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] wierd behavior of mdrun
How is it that the date and time is wrong? It is simply telling you that the simulation will be completed on Sep 16, using the time on the computer that the program is running on. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Fatal Equilibration Errors
You might want to consider the parameters I developed for propylene glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some guidance for you in terms of the parameterisation of ethylene glycol. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Suggestions for 3D-monitor/glasses for visualizing GROMACS output
Suggest you have a look and search the VMD emailing lists. These sorts of visualisation discussions come up from time to time with people sharing their experiences. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dean Cuebas Sent: Friday, 7 August 2009 3:42 AM To: gmx-users@gromacs.org Subject: [gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output Dear list, I know this might be a bit off topic. Sorry in advance. We have a grant app for upgrading our CRAY and I wanted to include the latest 3D visualization workstation to visualize my GROMACS trajectories. Any suggestions? LCD or CRT? Shutter glasses, no glasses? I am very new to this and haven't ever used a 3D workstation before, but I would very much any suggestions. Thanks very much for your help! Dean -- Dr. Dean Cuebas, Associate Professor of Chemistry deancue...@missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 ___ 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 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] Energy Minimisation and Equilibration Problems
Have you managed to minimise a single molecule? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Segmentation Fault (Address not mapped)
You indicate that I need to read the primary literature for the force fields. Could you please tell me where this literature can be found? I have searched using Google for the forcefields available for use in GROMACS (G43b1, G43a1, G43a2, G45a3, G53a5, G53a6, gmx), but have not found any primary literature for these force fields. Google |=| primary literature Use whatever journal search software your institution has, such as SciFinder, and look there. Some of the original papers are referenced in the manual too, I think. With regard to your comment about demonstrating that this force field is doing a good job at representing ammonia in the gas phase, how can I determine the diffusion of the pure ammonia gas? And what exactly do There is an appendix in the manual, lists all the scripts with GROMACS and what they can do. Have a browse through that. g_msd will do the job here. define in my .gro file, is it not? Also, the graphene is in an ammonia vapour, not in a vacuum, and the graphene structure is not infinite but has dimensions that fit well inside the simulation box. How would I determine if my graphene structure is stable? Run a simulation of the graphene and see if it does anything strange. You noted previously that it curled up, well, that is strange. And your graphene has to be infinite, otherwise, by definition, it isn't graphene. Something in the same class, which has n rings in the molecule. To handle graphene correctly you have to set it up so that it repeats across the PBC, like people set up with carbon nanotubes. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Energy Minimisation and Equilibration Problems
Maximum force = 9.4016180e+02 on atom 31 As has already been suggested, have you looked at the atoms listed as having the maximum force to see why? Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other). How are you visualising it? If using VMD, then it guesses the bonding based on how far things are apart. If your atoms are too close, then will appear like all bonded to each other. Sounds to me like there is something wrong with the box / molecule. Start with a box with only one molecule in it, see if you can equilibrate etc. Then build up from there so you can pin down where the issue is. ___ 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] Segmentation Fault (Address not mapped)
And, by the way, I have resolved the segmentation fault problem. It was being caused by the freezing of the graphene lattice. When I removed the freezing, I saw the graphene structure curl upward and am thinking that by freezing the atoms in place it was creating great forces between the atoms as they were kept from moving into their preferred orientation. Would you expect a real life graphene sheet to curl? Or should it be perfectly flat? This indicates that there are issues with the parameters used for describing the bonding within the graphene sheet. You have to go back and fix this before going any further. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Lincs Warning
Maximum force = 4.9815813e+24 on atom 169274 You should have a look at that atom, that is a large force. ___ 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] Fatal error
The error tells you what the problem is: Fatal error: reading tpx file (em.tpr) version 40 with version 20 program You are trying to read an em.tpr file that was generated using version 40 (as noted by the header it is GROMACS 3.3.1) using a version 20 program (as noted by the header it is GROMACS 3.0.5). You have to use a program that is at least 3.3.1 for it to work. Would be better if you were using the current 4.0.x version. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of s lal badshah Sent: Wednesday, 8 July 2009 8:17 AM To: gromacs Subject: [gmx-users] Fatal error Hi gromacs users, the other fatal error which is produces from my last year data is: s...@linux-g1cj:~/Desktop/283 g_rms -s em.tpr -f md283.trr -o md283-rmsd.xvg :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 3.0.5 (-: Copyright (c) 1991-2001, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_rms (-: Option Filename Type Description -s em.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f md283.trr Input Generic trajectory: xtc trr trj gro g96 pdb -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -n index.ndx Input, Opt. Index file -o md283-rmsd.xvg Outputxvgr/xmgr file -mirrmsdmir.xvg Output, Opt. xvgr/xmgr file -a avgrp.xvg Output, Opt. xvgr/xmgr file -dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file -m rmsd.xpm Output, Opt. X PixMap compatible matrix file -bin rmsd.dat Output, Opt. Generic data file -bm bond.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time -1 First frame (ps) to read from trajectory -e time -1 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]w bool no View output xvg, xpm, eps and pdb files -what enum rmsd Structural difference measure: rmsd, rho or rhosc -[no]pbc boolyes PBC check -[no]fit boolyes Fit to reference structure -prevint 0 Compare with previous frame -[no]split bool no Split graph where time is zero -skipint 1 Only write every nr-th frame to matrix -skip2int 1 Only write every nr-th frame to matrix -max real -1 Maximum level in comparison matrix -min real -1 Minimum level in comparison matrix -bmax real -1 Maximum level in bond angle matrix -bmin real -1 Minimum level in bond angle matrix -nlevelsint 80 Number of levels in the matrices Reading file em.tpr, VERSION 3.3.1 (single precision) Fatal error: reading tpx file (em.tpr) version 40 with version 20 program So now whats the main problem with this data: Regards, LAL BADSHAH Get your new Email address! http://sg.rd.yahoo.com/aa/mail/domainchoice/mail/signature/*http:/mail. promotions.yahoo.com/newdomains/aa/ Grab the Email name you've always wanted before someone else does! ___ 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] pdb does not work.
Because pdb2gmx has to know what residue(s) are contained in the .pdb file, and the third column identifies the residue and as the program has told you, it is called 1. And it does not have a 1 residue on the .rtp file associated with that forcefield. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] problem regarding removal of water from final simulation system.
Two ways: 1 - turn them off with the visualisation software you are using, only display the protein and lipid 2 - use editconf and the appropriate index groups Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma Sent: Thursday, 11 June 2009 3:19 PM To: gmx-users@gromacs.org Subject: [gmx-users] problem regarding removal of water from final simulation system. Dear all I have done successfully simulation of membrane protein , but after that to visualise my final model clearly I have to remove water molecules from my system (protein+lipid+water). But I have no Idea about the which command I should use to do this even it doesn't mentioned in justin,s tutorial also to make final pdb after simulation. So can anyone suggest me how to remove water form my final simulation system to make final pdb of only protein and lipid molecule? If anyone can help me I willbe really thankful for him/her. Nitu Sharma. Jawaherlal Nehru University New Delhi , India. ___ 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] Lipids forming unsual bonds
What exactly do you mean by unusual cross bonds? I suspect what you are seeing is simply a visualisation artifact, with a molecule being displayed across a PBC in the viewer you are using. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] mdp file for local pressure
The error message explicitly tells you what is wrong: Expected 2 elements for wall_atomtype, found 0 And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 On the wall_atomtype line, you have defined zero elements and you should have two. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Protein-Ligand Docking?
Just as Mark and Justin have said, this is up to you to define this question. The reason I said that, is you were asking how do I know if my molecule is docked to the protein?. The first step to answering that question is defining what you mean by being docked. Once you have a definition, then you can look at your molecule / protein and see if it fulfills those requirements. I don't do docking, but from what I have seen is that what is of interest is how well something fits into a pocket, proximity to some groups, and interactions between the molecule and the protein (hydrogen bonding and hydrophobic). You really need to search the literature, as others will be doing something similar. And docking has been going on for a long time. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem in simulation of DNA-protein complex
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma Sent: Wednesday, 13 May 2009 5:25 PM To: gmx-users@gromacs.org Subject: [gmx-users] problem in simulation of DNA-protein complex Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not found in residue topology database So , actually I am unable to understand what should I do to solve this . Is it possible to get DNA.itp file from anywhere .If anyone have Idea about this please help me. I really will be very thankful for him/her. Nitu sharma ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem in DNA simulation
Exact same question was answered just last month . http://www.gromacs.org/pipermail/gmx-users/2009-April/040974.html Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] lateral stress and surface tension
http://www.gromacs.org/pipermail/gmx-users/2006-December/024953.html Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of anirban polley Sent: Wednesday, 13 May 2009 3:11 PM To: gmx-users@gromacs.org Subject: [gmx-users] lateral stress and surface tension Dear Sir, I am analysing bilayer membrane. Could you please tell me how I can calculate stress and surface tension of the membrane? Thanking you, Anirban ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] local pressure
I would recommend you have a read through the appendix in the GROMACS manual titled Manual Pages. This has all the scripts provided with GROMACS and the manual page for them, which describes what each one does. Reading through that will go a long way to letting you know what you can and can't do with the GROMACS scripts. If can't find it there, then search at http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ (which is where I found the answer to your last question). Then, if after that, still can't find out how to do it, fire a question to this emailing list. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: RE: RDF in GMX 4 (Justin)
Run input file = .tpr Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Eudes Fileti Sent: Tuesday, 12 May 2009 6:33 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: RE: RDF in GMX 4 (Justin) Thanks for reply Justin. I had already read this part of the manual but I can´t understood it well. How can I take account the mentioned input file run? Would it be a kind of index file? Could you provide me an example? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC - CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 skype: eefileti http://fileti.ufabc.edu.br ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Protein-Ligand Docking?
First step, define what you mean by being DOCKed. Second step, determine if those conditions are meet by your protein and ligand. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Chih-Ying Lin Sent: Tuesday, 12 May 2009 7:37 AM To: gmx-users@gromacs.org Subject: [gmx-users] Protein-Ligand Docking? HI When i visualize the MD trajectory, the protein and ligand are closed by. But, I don't know if ligand really DOCK on the protein. Please tell me how to define the successful docking. Thank you Lin ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error by pdb2gmx
Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] ffgmx:diffusion of oxygen
The issue is you don't have enough statistics to get a meaningful result. Three ways you can get more, more particles, more time, or multiply runs. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sunil Thapa Sent: Tuesday, 28 April 2009 5:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] ffgmx:diffusion of oxygen Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostly not more than 10 ns. I also got to see your paper on dynamic property of water/alcohol mixture where you have used time less than 10 ns. Which msd curve is to take ? Another query : I want to simulate the system in a bit higher temperature 310 K . What are the parameters I should change in the mdp file. I saw the previous mails about it. Eric says that only time step should be small in order to constrain the bonds. Are there any other things? ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error by pdb2gmx
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44
RE: [gmx-users] Error by pdb2gmx
That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 9:24 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702
Re: [gmx-users] input the .gro and .trr file to the VMD
Best idea is to ask the vmd people, they have their own emailing list. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 28/04/2009, at 12:29 PM, He, Yang yang...@mavs.uta.edu wrote: HI Mark, I am indeed using the coarse-graining atoms .What do you mean by tell VMD to use suitable rules, or something similar. Do you have any fixed case about how to solve this problem in vmd? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: Monday, April 27, 2009 7:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] input the .gro and .trr file to the VMD He, Yang wrote: Hi all users, I want to get some snap shots from VMD through inputing my gro and trr file to the VMD. But I always find that I can not get the bond connection among the atoms and then, I try to use the dynamic bonds to solve this problem but another problem is that when I define a value for the cutoff distance, the bonds which don't exist among the atoms in the original shape will also come up . VMD guess at bonds based on atom names and inter-atomic distances, so your .gro file isn't following the rules it expects. Either your structures are broken, or they're coarse-grained and you need to tell VMD to use suitable rules, or something similar. Mark Except the dynamic method to figure out this problem, I wonder whether there are other ways to fix this problem. Thank you for any suggestions. Yang ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] say something about the pull geometry of cylinder
z-axis is the length of the cylinder, parallel to the straight sides. x-y is in the plane of the circle cross section of the cylinder. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of lammps lammps Sent: Friday, 24 April 2009 11:45 PM To: gmx-users@gromacs.org Subject: [gmx-users] say something about the pull geometry of cylinder Hi , I can not fully understand the picture of parameter of pull geometry of cylinder. Who can say something about it, Thanks in advance. Thanks in advance. - pull geometry cylinder Designed for pulling with respect to a layer where the reference COM is given by a local cylindrical part of the reference group. The pulling is in the direction of pull vec,which should have only a z-component. From the reference group a cylinder is selected for determining the COM, with the axis given by the x/y location of the group to be pulled and two radii. The radius pull r1 gives the radius within which all the relative weights are one, between pull r1 and pull r0 the weights are switched to zero. Mass weighting is also used. -- wende ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] grompp error
Both of those errors are telling you want you need to do. In your topol_A.itp file, there are no parameters for a particular proper dihedral. So, define one. Same with the next message. And it even tells you which line the issue is on in the .itp file, so very easy to track down which bonds are the issue and so on. I would recommend you read the errors, then check them against what is the wiki, then search the emailing list. Rarely does an error come up that has not been discussed and solved before. Many of the errors you are encounting are nothing out of the ordinary. And the non-zero charge, well being non-zero is not a real issue. What is the real issue is that it is a non-integer. If it was an integer, then that simply means you need counter ions. But being non-integer means you have a problem with the charges on that atoms in your topology. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma Sent: Friday, 24 April 2009 2:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] grompp error Dear MARK Now the problem of matching of topology file and coordinate file solved but the other two errors come during running grompp in the second step of inflategro . my command line is like this- grompp -f em.mdp -p topolinflate.top -c inflated_system.gro -o inflated-em.tpr the error came is like this- ERROR 1 [file topol_A.itp, line 29912]: No default Proper Dih. types ERROR 2 [file topol_B.itp, line 26604]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 3 bonded neighbours molecule type 'DMPC' NOTE 1 [file topolinflate.top, line 33]: System has non-zero total charge: -1.161999e+01 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.3 Source code file: grompp.c, line: 986 Fatal error: There were 2 errors in input file(s) --- can you suggest me what is the possible way to solve this problem and in case of note - system has non zero charge how can i make its neutral? ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf
That is entirely up to you. The forth paragraph in the help explains how the three atoms in the index are used to generate the coordinate system. Best idea with anything like this, have a play, see what comes out, see if it is what you want, then try again. Play with it like that will also help get further understanding of what is going on. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Membrane protein tutorial
Well, as the error says, popc isn't defined in the index file. Seems grompp is looking for a popc entry in the index file, and can't find it. So, I would hazard to say, you need to define it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pawan Kumar Sent: Thursday, 9 April 2009 2:39 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Membrane protein tutorial Hello sir, Thanks for such a explanatory tutorial. I am stuck with one error now. I have protein, popc, sol and cl- in my system. I have merged the sol and cl- using make_ndx. But when I run grompp I get the error like this popc not defined in the index file. The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o box_pr.tpr Any suggestions please. pr.mdp file : title = protein in popc bilayer cpp = /usr/bin/cpp define = -DPOSRES -DPOSRES_LIPID constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1 vdw-type= Cut-off rvdw= 1 ; Berendsen temperature coupling is on in two groups tcoupl = berendsen tc_grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps= Protein POPC SOL_CL- ; Pressure coupling is on ;Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanking you, Pawan ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf
What exactly your issue with using g_sdf? You need to supple a trajectory, index, and topology. Index contains the three reference atoms for the molecule, plus the atom you are calculating the sdf to. Selection of the correct grid size and binwidth is required to get something that looks as you want it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] density around protein
Or g_sdf Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] editing .rtp files
Another to keep an eye out for, is make sure that you edited the correct .rtp file you tell pdb2gmx to use when running it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem in topology file for protein+lipid bilayer system
May be have bit of a read of http://wiki.gromacs.org/index.php/Category:Force_Fields and the manual, so you can get a grip on what forcefields actually are and how you use them. I get the impression you are trying to do things here without actually understanding or even thinking about what you are doing. Things are NOT plug and play here, you actually have to think and work things out. Take a step back for a moment, do some reading, have a play with some tutorials, then go back and address the problem you looking to research. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How to calculate the dihedral angle variations ???
g_angle will do that fine, and with the options you used it should have done so. Possible issue that may make that fail is you failed to generate the correct angle index file for the dihedral(s) of interest. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Venkat Reddy Sent: Wednesday, 1 April 2009 7:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to calculate the dihedral angle variations ??? Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all Please suggest me the right options Thanks for ur concern 2009/4/1 Tsjerk Wassenaar tsje...@gmail.com Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what exactly it is you want. We need that sort of information to be able to help you out. Cheers, Tsjerk 2009/4/1 Venkat Reddy venkat...@gmail.com: First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. antonia_h...@hotmail.com Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the Cβ-S-S-Cβ (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messages ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR,
RE: [gmx-users] grompp error in running simulation of lipid bilayer
Might I suggest that you refer to this webpage http://wiki.gromacs.org/index.php/Errors It would have answered both of your error questions you have posted. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] (no subject) - fluctuations
Is there a way to reduce the fluctuations of the properties calculated with g_energy? Fluctuations scale as 1/sqrt(N) where N is the number of molecules. So the answer is yes. Depending on what you actually want to do, some smoothing of the data may be what you are after. One way of doing this is taking some points before and after a time, then averaging them all together. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Cross-linking of polymers
Kim, Recently I have been focusing on cross-linking phenomenon of polymers. As far as I understood, cross-linking include bond breaks in one polymer chain and bond occurrences among broken chains. I guess OPLS-aa is not suitable for this purpose, and my question is this. Is my guess correct? OPLS-aa is for molecular dynamics, no bond breaking or formation can happen, so you cannot use it when you that happening. If so, what others can be used for this purpose? ReaxFF or RWFF? Appears so, http://en.wikipedia.org/wiki/Force_field_(chemistry)#Reactive_Force_Fiel ds You really need to do a literature search and see what others doing similar things are using etc. Additionally, should I combine those potentials (ReaxFF or RWFF) with OPLS-aa force fields to mimic cross-linking (comes from RWFF etc.) of a realistic polymers (comes from OPLS-aa)? Depends on the other forcefield and if it has been derived and is compatible with OPLS-aa. Read point 1 on this page http://wiki.gromacs.org/index.php/Parameterization Without having read about those forcefields, highly unlikely that you can mix them. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_rdf program
No, the molecule has not gone out the side of the box and not entered the other side. If you check the solvent on the opposite side of the box, you will notice that there is a big hole that exactly matches up with the DNA fragment that is sticking out. Use the pbc options in VMD to display neighbouring images of the box, that will make it much more explicit what is going on. Unless otherwise noted, the analsysis programs and intelligent enough to realise where things are located. Remember, with a periodic box, all things are relative. The location of the boundaries of the base unit are totally arbitary, you can move them around at your will to visualise, it makes no difference to how things are calculated or handled by the software. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pablo Umazano Sent: Thursday, 19 March 2009 10:19 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_rdf program Hello, I am relatively new to gromacs and I really would appreciate help with the following question. I have used a coarse-grained model to represent a DNA fragment with approximately 50 nm of length. I have run a Langevin dynamics simulation of DNA with ions NA+ and CL- to study their distribution of around DNA. During simulation I used the option to remove the center of mass motion (default option) because when there are no external forces the com linear moment must be conserved. Now, I want study the redistribution of ions around DNA when an external electric field is applied. My doubt is the following: when external electric field is applied, should I remove the center of mass motion? I thought that the answer was no, then I tried the following option: comm_modenone but half of DNA goes out of the box during simulation (I see this with ngmx and in out.gro) and nothing enters the another side. I know gromacs use pbc to calculate the interactions between particles, but I wonder if g_rdf program considers that part of DNA is out the box to calculate the radial function distribution of ions around DNA. Thank. Pablo ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Possible to stop mdrun changing file names whenusingcheckpoint files?
Berk that would be handy. Option in that, could you may be have not to change the name at all and use the names specified on the command line? Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 17/02/2009, at 6:01 PM, Berk Hess g...@hotmail.com wrote: Date: Tue, 17 Feb 2009 16:59:42 +1100 From: dallas.war...@pharm.monash.edu.au Subject: RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files? To: gmx-users@gromacs.org Chris, One option is to avoid checkpoint files all together. I personally use a grompp/mdrun cycle of ~2h segments that was historically done in order to utilize the -sort -shuffle options to gromacs 3. I found it simpler to keep on doing the exact same thing in gromacs 4, even though I no longer -sort or -shuffle. It appears to be working fine for me. I suspect that you could do the same type of thing via tpbconv. Yes, that is what I was doing previously and are continuing to do so with some at the moment with 4.0.X I suppose the question is now, is it a more continuous simulation to be using the checkpoint files, or does tpbconv with the energy and trajectory files provide the same degree of accuracy? The trajectory and energy file do not store all the state variables for all thermostats and barostats. But resetting these variables introduces such a small error in most cases that it is negligible. I think I'll add a -rename (or something like that) flag to mdrun, so you can control the renaming. Berk Totally unrelated and a little nugget for people that happen to have an iPhone or iPod touch, you can get an application called Molecules for free that allows you to view .pdb files, download direct from the pdb database or from custom location. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation Express yourself instantly with MSN Messenger! MSN Messenger ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Difference between command pdb2gmx and pdb2gmx_d
The _d denotes that the command is the double precision version. Command does exactly the same things, just at double precision which may or may not make any difference to the result. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 18/02/2009, at 9:57 AM, Peggy Yao peggy@gmail.com wrote: Dear all, In the manual, almost all commands have 2 versions: command and command_d. For example, pdb2gmx, and pdb2gmx_d. What is the difference? I searched in both the manual and the internet, but was not able to find the answer. Thanks! Peggy ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to show the created box?
There is a script in vmd to do it. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 16/02/2009, at 3:30 PM, Chih-Ying Lin chihying2...@gmail.com wrote: HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the box is not shown. how can i show the created box with VMD? thank you Lin ___ 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] The difference about NPT and NVT ensemble.
I have some questions about ensemble. Would you please tell me about NPT or NVT ensemble? What difference about them? http://wiki.gromacs.org/index.php/Molecular_Dynamics_Simulations Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Continuation of Runs and Checkpoint File Use
OK, well I got this wrong. If you want to extend or continue a simulation that has completed, you still have to use tpbconv. It is used to change the number of steps, then you feed that into mdrun with the checkpoint file. The only time you don't need tpbconv now is with a crashed simulation. I have added the information here: http://wiki.gromacs.org/index.php/Extending_Simulations Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?
When using checkpoint files to continue a run, mdrun overrides the output file names specified by putting .part before the file extension. I don't want it to do that, since I have already told it how I want the output files to be named. Is it possible to stop that happening? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
