[gmx-users] Membrane protein MD Simulation
Dear Yanzi, Thank you for your swift response. I did all you wrote to me. Also I include ffG43a1 forcefield in the lipid.itp file and then include the lipid.itp file in the protein.top at line 12 as forcefield parameter. When I run grompp the following error appeared: Fatal erroe; Invalid order for directive moleculetype, file "protein.top", line 14 What is this error and what do I have to do? Thank you in advance for your valuable aid. Best regards, Behnoush Zare Iran University of Medical Sciences, Department of Pharmacology --- Dear Yanzi zhou, I am a new gromacs user and reading your message sent by gmx-users in my mail box I found that you have worked on lipid bilayer simulation. My outlook express is out of work so I had to mail to you directly. Sorry about I don’t have any response to your question my problem is a protein-lipid bilayer simulation. I am trying to perform MD Simulation on a membrane protein within the lipid bilayer, popc. I have the .pdb and the .top file of the protein. Also I have got the popc.pdb, popc.itp and lipid.itp files from the site of Dr. Tieleman at the Calgary University. I have visited the www.wiki.gromacs.org site, specially the lecture of Gromacs tutorial for membrane protein simulations by Dr. Phil Biggin, but that is not enough to running the simulation. For example after creating the pdb file including protein and popc what is the top file to running grompp. Would you please kindly provide me the step by step method for performing MD Simulation on a protein within lipid bilayer. Thank you in advance for your valuable help. I am looking forward to hearing from you. Best regards, Behnoush Zare Iran University of Medical Sciences, Department of Pharmacology Hello, Behnoush: I'm glad to help you though I'm a green hand myself. You should create the topology file for lipids by yourself. For example, if you do simulation for lipids only, first, copy lipid.itp and popc.itp to the ~/GROMACS/share/top/, then if you have included other force field in your top file, such as ffgmx.itp, open lipid.itp, delete the two lines: [ defaults ] 1 1 and then prepare the top file for lipids by yourself. Following is an example for POPE: ; ; ; Include forcefield parameters # include "ffgmx.itp" # include "lipid.itp" ; Include water topology #include "spc.itp" ; Include topology for lipids #include "pope.itp" [ system ] ; Name POPE in water [ molecules ] ; Compound#mols POPE 340 SOL 6729 If you do simulation for lipids and protein, first, you can create the top file for protein using pdb2gmx, then in the top file, you may add such lines at the bottom: ; Include topology for lipids #include "pope.itp" [ system ] ; Name Protein in POPE [ molecules ] ; Compound#mols Protein 1 POPE 340 SOL 6729 Best wishes. - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS and GPU (and PS3)
Hi everybody, I wonder if GROMACS will eventually support running on the graphics cards, especially since there have been several announcements of extremely powerful cards like AMD's FireStream recently. I know that the question has repeatedly been asked some time ago, but hey, the Stanford guys from [EMAIL PROTECTED] did manage to adapt GROMACS for GPUs, and they don't seem to regret it :) I'd also like to know if anyone has actually tried running GROMACS on PlayStation 3, seems like this Cell CPU could perform really well for moderately sized systems (so that you don't run into the 512 MB memory limitation)... Best regards, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rtp
On Fri, 14 Dec 2007 14:27:10 -0800 Arthur Roberts <[EMAIL PROTECTED]> wrote: Dear Jayant, I might be wrong, but I think the original gmx force field that you are referring to has been deprecated. This is correct. It is better to use the OPLS FF if you like to include hydrogens in your description of the protein. You also have the option to run with the GROMOS FF and then add the proton with "protonate". XAvier Best wishes, Art On Dec 14, 2007, at 1:44 PM, jayant_jacques wrote: Hi! I am attempting to simulate a protein with a modified amino acid using the Gromacs force field with hydrogens for NMR. I have built the RTP and TOP files using PRODRG. I need to know what is the rtp file? relevant to the above force field such that I can append my rtp file. Is it the ffgmx2.rtp or ffgmx.rtp? Thanks Jayant James Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Membrane protein MD Simulation
Behnoush Zare wrote: Dear Yanzi, Thank you for your swift response. I did all you wrote to me. Also I include ffG43a1 forcefield in the lipid.itp file and then include the lipid.itp file in the protein.top at line 12 as forcefield parameter. When I run grompp the following error appeared: Be careful mixing two force fields unless you know what you are doing, i.e. other people have published with this mix. See http://wiki.gromacs.org/index.php/Force_Fields#Usage Fatal erroe; Invalid order for directive moleculetype, file "protein.top", line 14 What is this error and what do I have to do? This means the directives in the .top file (possibly via an .itp #include) are out of order. Directives look like "[ moleculetype ]". See chapter five of the GROMACS manual for the order in which they need to appear. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with npt
I wrote yes to generate velocity. Can that be a reason for the problem? Since I am doing membrane simulation it is advised to do production runs in npt thats the only other difference. > Date: Sat, 15 Dec 2007 06:03:27 +1100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] problem with npt > > pragya chohan wrote: > > > > thanks for your help. > > My system ran fine for 250 ps but later the bilayer deformed very much. > > What was your system preparation protocol - i.e. minimization and > equilibration? See > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.asp?pid=220___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with npt
Quoting pragya chohan <[EMAIL PROTECTED]>: > > > I wrote yes to generate velocity. Can that be a reason for the problem? Since > I am doing membrane simulation it is advised to do production runs in npt > thats the only other difference. I think what Mark was asking for was a bit more detail on how you put your system together. It would be helpful to know (step by step) what you did, as that may highlight a problem. Also, what do you define as "deformed very much?" Some fluctuations are to be expected, and 250 ps is a relatively short time frame. In some of my bilayer simulations, the lipids look quite strange under NVT, but after a nanosecond or two or NPT they even out and behave normally. -Justin > > > Date: Sat, 15 Dec 2007 06:03:27 +1100 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] problem with npt > > > > pragya chohan wrote: > > > > > > thanks for your help. > > > My system ran fine for 250 ps but later the bilayer deformed very much. > > > > What was your system preparation protocol - i.e. minimization and > > equilibration? See > > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation > > > > Mark > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _ > Post free property ads on Yello Classifieds now! www.yello.in > http://ss1.richmedia.in/recurl.asp?pid=220___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with npt
i started with the lipid coordinates from peter tieleman and removed the water. then i added water by genbox. I did energy minimization followed by position restrain, which I removed gradually. all of it was done under npt. I carried out npt for 250 ps. During the next 250 ps npt run the bilayers separated and deformed. > Date: Sat, 15 Dec 2007 09:53:06 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: RE: [gmx-users] problem with npt> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> >> > I wrote yes to generate velocity. Can that be a reason for the problem? Since> > I am doing membrane simulation it is advised to do production runs in npt> > thats the only other difference.> > I think what Mark was asking for was a bit more detail on how you put your> system together. It would be helpful to know (step by step) what you did, as> that may highlight a problem. Also, what do you define as "deformed very> much?" Some fluctuations are to be expected, and 250 ps is a relatively short> time frame. In some of my bilayer simulations, the lipids look quite strange> under NVT, but after a nanosecond or two or NPT they even out and behave> normally.> > -Justin> > > > > > Date: Sat, 15 Dec 2007 06:03:27 +1100> > > From: [EMAIL PROTECTED]> > > To: gmx-users@gromacs.org> > > Subject: Re: [gmx-users] problem with npt> > >> > > pragya chohan wrote:> > > >> > > > thanks for your help.> > > > My system ran fine for 250 ps but later the bilayer deformed very much.> > >> > > What was your system preparation protocol - i.e. minimization and> > > equilibration? See> > > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation> > >> > > Mark> > > ___> > > gmx-users mailing list gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/search before posting!> > > Please don't post (un)subscribe requests to the list. Use the> > > www interface or send it to [EMAIL PROTECTED]> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > _> > Post free property ads on Yello Classifieds now! www.yello.in> >> http://ss1.richmedia.in/recurl.asp?pid=220___> > gmx-users mailing list gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/search before posting!> > Please don't post (un)subscribe requests to the list. Use the> > www interface or send it to [EMAIL PROTECTED]> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > > > > > Justin A. Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > > ___> gmx-users mailing list gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED]> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Post ads for free - to sell, rent or even buy.www.yello.in http://ss1.richmedia.in/recurl.asp?pid=186___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Membrane protein MD Simulation
Dear Behnoush: I think it is because the lipid.itp is a mixture of lipid and ffgmx parameters. Different force field uses different labels for molecules and atoms. Try using ffgmx instead of ffg43a1, and find out if the problem will be resolved. Sincerely, Yanzi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] coupling to water bath
Dear Users I have a system in of protein with in bound chlorine ion. I also added Na ion to the system to neutralize charge on system. I have to couple the system to water bath. can i couple protein chlorine and Na together and solvent separately? or should i couple protein and chlorine together and solvent and na together? I the later case -n option would take in 2 index files. then what should I do? Thanks in advance _ Tried the new MSN Messenger? It’s cool! Download now. http://messenger.msn.com/Download/Default.aspx?mkt=en-in___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coupling to water bath
Quoting pragya chohan <[EMAIL PROTECTED]>: > > Dear Users > I have a system in of protein with in bound chlorine ion. I also added Na ion > to the system to neutralize charge on system. I have to couple the system to > water bath. can i couple protein chlorine and Na together and solvent > separately? or should i couple protein and chlorine together and solvent and > na together? You could do either. Try make_ndx -h. But generally, when I simulate a protein in water and ions, I simply couple the whole system to the same bath. See here: http://wiki.gromacs.org/index.php/Thermostats > I the later case -n option would take in 2 index files. then what should I > do? Specify both groups within the same index file. Again, make_ndx -h. Type 'help' for some examples. -Justin > Thanks in advance > _ > Tried the new MSN Messenger? Its cool! Download now. > http://messenger.msn.com/Download/Default.aspx?mkt=en-in Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] determining of Kn and Posn in Umbrella sampling
Hi dear I want to compute PMF between two amine molecoules by umbrella sampling but I do'nt know Kn and Posn in umbrella samplig how are determining. if you are having points please help me. Thanks in advance - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
