Re: [gmx-users] Ionic liquids

Hi, nice to hear that someone else is also interested in doing MD in room temperature ionic liquids. What kind of ions do you use? Bmim chlorides perhaps, or do you have a larger counterion to bmim? Or a completely different cation? As Mark pointed out, if you do not have a properly parameter

[gmx-users] Freeze groups and rotation

Freezing fixes atoms in place in at least 1 dimension. If one fixes atoms in place in all 3 dimensions, can they still rotate? In particular, if one fixes the oxygen atoms of water in place, can the hydrogens still rotate? And how does making hydrogens into virtual sites affect this? Is the case d

Re: [gmx-users] The energy minimization....

> Hi, everyone:I have meet some problem when simulating a protein and > ATP complex. The energy minimization will stop after 14 steps. I had > followed Mark's suggestion, did the protein and ATP eneryg minimization > independently, and  found that the protein can finish its > minimization correctly

[gmx-users] The energy minimization....

Hi, everyone:I have meet some problem when simulating a protein and ATP complex. The energy minimization will stop after 14 steps. I had followed Mark's suggestion, did the protein and ATP eneryg minimization independently, and  found that the protein can finish its minimization correctly, but  the

[gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

On top of Mark's point, many programs in GROMACS uses suffix to determine the file type. To use those files with name beginning #, you shall remove the leading and trailing # in the filename by renaming. In some cases you may not want to rename a file. In this case you can use a symbolic lin

Re: [gmx-users] Ionic liquids

> On 8/16/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > What a coincidence! > A student in the biology major come to me he want to do simulation with > ionic liquid. > I have much doubt about that kind of simulation but becase he is eager to > do > it. > I try to make the solvent by placing the mo

Re: [gmx-users] Ionic liquids

On 8/16/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Sampo Karkola wrote: > > Dear all, > > > > I was wondering if there are any parameters defined for ionic liquids? > > Some enzymes have retained their activity when the solvent has been a > > mixture of water and ionic liquids and it would be

Re: [gmx-users] hi

On 8/15/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > vinod kumar wrote: > > Hi, gmx-users, > > > > HI , how to overcome this problem > > the output after grompp if em.mdp > >> fatal error : number of coordinates in coordinate file ( solvated.gro8655) > >> does not match topology ( t

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

Thank you for the good reference. ^^ On 8/14/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > > > > > JCTC December 2005, IIRC :-) > > > > YDRC...: JCC 26: 1701-1718 (December 2005) :p > > Tsjerk > > > > Mark > > ___ > > gmx-users mailing listgmx-us

Re: [gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

On 8/16/2007 9:53 AM, Mark Abraham wrote: huifang liu wrote: I typed this command: grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_em.tpr It responded to me like this:Invalid command line argument: speptide_empdb.tpr I am a new -learner.Can you tell me where the problem is.

Re: [gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

huifang liu wrote: I typed this command: grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_em.tpr It responded to me like this:Invalid command line argument: speptide_empdb.tpr I am a new -learner.Can you tell me where the problem is. Backslashes are used to "escape" charact

[gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

I typed this command: grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_em.tpr It responded to me like this:Invalid command line argument: speptide_empdb.tpr I am a new -learner.Can you tell me where the problem is. Thanks. ___ gmx-user

Re: [gmx-users] Potential energy contributions and total pot ener (2)

[EMAIL PROTECTED] wrote: Dear community, Thanks, Mark! But I can't find any g_energy or log file terms specifically related to solvent bonded energy (bonds and angles). The log file bonded terms are for the total system, I guess, but they are very close to the ones I get when I request their "pr

Re: [gmx-users] Re: learning gromacs question

David van der Spoel wrote: On Wed, 15 Aug 2007, burkhard rammner wrote: Dear David, although I am a former biochemist (and do now 3D productions for scientific purposes) I never came in contact with MD before. Besides my "normal" molecule visualisation stuff I now try to do protein folding w

Re: [gmx-users] Potential energy positive. Can be?

Eudes Fileti wrote: Hi gmx users, I have tried to simulate a box with 1000 molecules of toluene and I always have obtained a positive value for the potential energy. I have used three different models of potential (with and without 14 interactions) and all of them provides a positive value for

[gmx-users] Pull code methods?

Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rat

[gmx-users] Potential energy contributions and total pot ener (2)

Dear community, Thanks, Mark! But I can't find any g_energy or log file terms specifically related to solvent bonded energy (bonds and angles). The log file bonded terms are for the total system, I guess, but they are very close to the ones I get when I request their "protein" counterpart from g_e

Re: [gmx-users] how to build up fixed connections? How to simulate no electrostatics?

Erik, thanks for the quick and clear answer! Of course I should have known in advance that you guys have thought of everything, and even implemented separate loops for every single type of interaction that can come into play. ;-) Greetings, Jeroen >Date: Wed, 15 Aug 2007 20:49:46 +0200 >From: E

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Hi Jeroen, Just set the charges to zero - then the program will automatically detect it and use LJ-only loops everywhere. Cheers, Erik On Aug 15, 2007, at 8:12 PM, van Bemmelen wrote: Hi all, As a side note: although I also have some trouble figuring out what Nicolas Schmidt is exactly t

[gmx-users] Re: learning gromacs question

On Wed, 15 Aug 2007, burkhard rammner wrote: > >Dear David, > >although I am a former biochemist (and do now 3D productions for >scientific purposes) I never came in contact with MD before. >Besides my "normal" molecule visualisation stuff I now try to do protein >folding with gromacs. > >What I

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Hi all, As a side note: although I also have some trouble figuring out what Nicolas Schmidt is exactly trying to do, I find the question "what to do to totally switch the electrostatics off?" to be quite intriguing. It is my understanding that when you simply set rcoulomb=0, this actually means an

Re: [gmx-users] Re:

You should look at the ATP topology and see if the parameters you are using look sensible. Where did you get the topology from, did you use the united atom one already in the GROMOS96 ff? Also did grompp give you any warnings before your minimisation? Tom --On Thursday, August 16, 2007 01:04:

[gmx-users] Potential energy positive. Can be?

Hi gmx users, I have tried to simulate a box with 1000 molecules of toluene and I always have obtained a positive value for the potential energy. I have used three different models of potential (with and without 14 interactions) and all of them provides a positive value for energy. I must be fallin

Re: [gmx-users] Ionic liquids

Sampo Karkola wrote: Dear all, I was wondering if there are any parameters defined for ionic liquids? Some enzymes have retained their activity when the solvent has been a mixture of water and ionic liquids and it would be interesting to study the actual catalytical reactions in such a solven

Re: [gmx-users] Replica exchange method

priya priya wrote: Dear all, i want to start with the replica exchange method in gromacs, but i am not able to search the script for that in the program. Can anybody tell me by what name it is in the program and the location, as i want to look into the program before starting. Please describ

[gmx-users] Re:

[EMAIL PROTECTED] wrote: > Dear Mark: Please keep correspondence on the list for others to see and use. > Thanks for your help about my problem of running GROMACS energy minimization. > I do what you suggestion, and the protein's minization seems to be correct, > it run > about 300 steps and t

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Nicolas Schmidt wrote: (a) Nope, my .mdp-file don't reads that. So I think I don't use one. (b) I use some different software, that does exactly what I want. It's very reliable and it's telling me that the pressure of a 2CLJ-fluid with all the set parameters should be different. Since I wanna d

Re: [gmx-users] Potential energy contributions and total pot ener

[EMAIL PROTECTED] wrote: Dear community, I am trying to figure out how potential energy contributions sum up to the total potential energy. With g_energy, I can get the following energy contributions of my solvated protein system: a) protein-protein b) protein-solvent c) solvent-solvent I have

Re: [gmx-users] Replica exchange method

Have a look at GMX/src/kernel/repl_ex.c priya priya wrote: Dear all, i want to start with the replica exchange method in gromacs, but i am not able to search the script for that in the program. Can anybody tell me by what name it is in the program and the location, as i want to look into the

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

(a) Nope, my .mdp-file don't reads that. So I think I don't use one. (b) I use some different software, that does exactly what I want. It's very reliable and it's telling me that the pressure of a 2CLJ-fluid with all the set parameters should be different. Since I wanna do the exact same thing,

[gmx-users] Potential energy contributions and total pot ener

Dear community, I am trying to figure out how potential energy contributions sum up to the total potential energy. With g_energy, I can get the following energy contributions of my solvated protein system: a) protein-protein b) protein-solvent c) solvent-solvent I have two questions: 1) I gues

[gmx-users] Ionic liquids

Dear all, I was wondering if there are any parameters defined for ionic liquids? Some enzymes have retained their activity when the solvent has been a mixture of water and ionic liquids and it would be interesting to study the actual catalytical reactions in such a solvent. I'm not an expert

[gmx-users] Replica exchange method

Dear all, i want to start with the replica exchange method in gromacs, but i am not able to search the script for that in the program. Can anybody tell me by what name it is in the program and the location, as i want to look into the program before starting. Regards ---