Re: [gmx-users] problems with rerun

rsf wrote: Mark Thanks for your reply, I do prepare a .tpr file for each run. I run the original md run and then I run grompp using the files with my modified topology I need and then run with the -rerun option as you said. I am using gromacs 4.0.5 since I saw in the notes for the release it had

[gmx-users] Re: Something about getting started

DreamCatcher wrote: Dear Justin, I did make the rtp and hdb files in accordance with the tutorial onthe website http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

[gmx-users] Re: gmx-users Digest, Vol 64, Issue 156

an/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.gromac

Re: [gmx-users] problems with rerun

Mark Thanks for your reply, I do prepare a .tpr file for each run. I run the original md run and then I run grompp using the files with my modified topology I need and then run with the -rerun option as you said. I am using gromacs 4.0.5 since I saw in the notes for the release it had been fixed. I

Re: [gmx-users] problems with rerun

rsf wrote: Hi I have a molecule described by two sets of parameters (in atom connectivity and coupe values of bond interactions) and I need to get the energy difference between those two descriptions. I have been having problems with the rerun capability (I am using the latest version of gromacs)

Re: [gmx-users] [Fwd: Please solve my problem]

ceste...@unsl.edu.ar wrote: Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. If there actually is no

Re: [gmx-users] Parameters for membrane stability

Ragnarok sdf wrote: I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC from tieleman's website as a starting structure. I've run a short 1 ns semi-isotropic simulation at 323 K and monitored the area per lipid as a stability parameter for my membrane simulation. If the area

[gmx-users] problems with rerun

Hi I have a molecule described by two sets of parameters (in atom connectivity and coupe values of bond interactions) and I need to get the energy difference between those two descriptions. I have been having problems with the rerun capability (I am using the latest version of gromacs) I did the

[gmx-users] Parameters for membrane stability

I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC from tieleman's website as a starting structure. I've run a short 1 ns semi-isotropic simulation at 323 K and monitored the area per lipid as a stability parameter for my membrane simulation. If the area per lipid maintains the sa

Re: [gmx-users] correlation function

Jamie Seyed wrote: On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul > wrote: Jamie Seyed wrote: with a lot of x-y sets seperated by & character. I think I did not get the key point here. So my question is what is the right way to get

Re: [gmx-users] correlation function

On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > > with a lot of x-y sets seperated by & character. I think I did not get the >> key point here. So my question is what is the right way to get >> using this tool?? Many Thanks/Jamie >> > > Well, as far as g_analy

Re: [gmx-users] correlation function

Jamie Seyed wrote: with a lot of x-y sets seperated by & character. I think I did not get the key point here. So my question is what is the right way to get using this tool?? Many Thanks/Jamie Well, as far as g_analyze is concerned, it's done its job. If you feed g_analyze a whole bunch

Re: [gmx-users] correlation function

On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul wrote: > > > >Actually when I open autocorr.xvg I can see from data/feature >>extraction/ the last set is S1295 (N=101, autocorr.xvg) which means >>they are 1296 graphs each with poor statistics start at 1 and coming >>down. To ha

Re: [gmx-users] Something about getting started

DreamCatcher wrote: Dear gmx-users, I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol simulation.But I don't even know how to start it. Then start simple with some tutorial material: http://oldwiki.gromacs.org/index.php/Tutorials Is it necessary to start my s

[gmx-users] Something about getting started

Dear gmx-users, I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol simulation.But I don't even know how to start it. Is it necessary to start my simulation with a .pdb files?If so,What should I do before this?I can make an pdb file for a chain of syndiotatic polyvinyl-

Re: [gmx-users] [Fwd: Please solve my problem]

Hi again the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1 distribution thanks Carmen > > ceste...@unsl.edu.ar wrote: >> Hi All >> I have similar problem using gromacs 4.0.2. >> The MD simulation (5 ns) on single processor is complited in 5 days, but >> the same MD can`t be c

Re: [gmx-users] [Fwd: Please solve my problem]

ceste...@unsl.edu.ar wrote: Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appre

Re: [gmx-users] spc model of water

abhijit kayal wrote: Hi, Myself Abhijit Kayal.Please anyone can give me the right topology,grompp and conf file of spc model of water. The coordinate and topolgy file for SPC water is provided in the /share/top subdirectory of your Gromacs installation. There is no standard grompp inpu

RE: [gmx-users] results of tpi

Hi, Did you try to load the file into xmgrace? That will give you more readable output. I don't know what you mean with Psi. s2 is , where U is the interaction energy between the inserted molecule and the system. V is the volume of that frame. The entry s4 gives the average potential energy: . T

Re: [gmx-users] [Fwd: Please solve my problem]

Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appreciated Carmen > > To, >D

[gmx-users] spc model of water

Hi, Myself Abhijit Kayal.Please anyone can give me the right topology,grompp and conf file of spc model of water. Abhijit Kayal IIT Delhi ___

[gmx-users] results of tpi

Hi everybody, I'm doing calculations with results, that I receive from tpi insertions. As I don't get the results I am heading for, I starded to wonder weather I interpretate the values in the columns of the xvg file correct. Hear is the head of the xvg files and next to it my interpretation of

RE: [gmx-users] RE: Re: Pull to separate dimer

; -- > > > 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/just

Re: [gmx-users] topology file

abhijit kayal wrote: Hi, Myself Abhijit Kayal,student at IITD.Is it possible to create a topology file by Amber or some other molecular dynamics software for nonstandard molecules such as n-butane and can these topology files be used in gromacs?please reply. Yes. There are scrip

[gmx-users] topology file

Hi, Myself Abhijit Kayal,student at IITD.Is it possible to create a topology file by Amber or some other molecular dynamics software for nonstandard molecules such as n-butane and can these topology files be used in gromacs?please reply. Abhijit Kayal

[gmx-users] RE: Re: Pull to separate dimer

-- > > > > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users

RE: [gmx-users] p-lincs use

Hi, I don't understand what you want or why you want this. If it is necessary (you have constraint in your molecule between different charge groups and you run in parallel with domain decomposition) Gromacs will automatically use P-LINCS. Berk > Date: Mon, 24 Aug 2009 19:24:32 +0800 > From: dcp

[gmx-users] p-lincs use

Dear Gromacs developers, I am using the Gromacs 4.05 and I want use the P-LINCS in my work. But I donot know how to use it. Could you please give me a detailed description of using it, as I cannot find its use method in the Manual4.0 Thank you very much in advance, > James, Wang (Dr.)

RE: [gmx-users] Re: Pull to separate dimer

> Date: Sat, 22 Aug 2009 20:01:19 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: Pull to separate dimer > > > > Ragnarok sdf wrote: > > Hi Justin, yes the intention is to pull the dimer apart within the > > plane of the bilayer. I've ran a few