[gmx-users] regarding visualizing the output

hello sir, 1.i ran simulation for 2 ns.i want to view the structure from 1500 to 2000 frames at every 25 ps.how to get it in pdb strucutres of the above wanted frames. 2.with the use of trjconv i had one pdb file converted from one frame. i'm viewing that structure with VMD, but when i'm

Re: [gmx-users] I want to stop this group

Pakpoom Utta wrote: thanks Express yourself instantly with MSN Messenger! MSN Messenger _

[gmx-users] I want to stop this group

thanksExpress yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send

Re: [gmx-users] position and velocity in traj file & Verlet algorithm in GROMACS 3.3

Jianwei Wang wrote: Two questions: (1) What are the positions and velocities stored in trajectory files by gmx3.3? I know the positions must be at current time (at time t), but how about velocities? are they at t-0.5*dt, t+0.5*dt or estimated at time t? If gmx3.3 uses leap-frog form of verlet, v

Re: [gmx-users] special molecule

Dongsheng Zhang wrote: Sear Mark, Since PRODRG server only generates a itp file by using gromos type force field, do I have to use gromos force field for my whole protein-ligand system if my ligand force field parameters are got from PRODRG? In another word, can I mix two different force field (

Re: [gmx-users] special molecule

Tamas Horvath wrote: So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple? The order of the [ molecules ] section will have to correspond to the order in the structure file you supply with -c to grompp, but if y

[gmx-users] position and velocity in traj file & Verlet algorithm in GROMACS 3.3

Two questions: (1) What are the positions and velocities stored in trajectory files by gmx3.3? I know the positions must be at current time (at time t), but how about velocities? are they at t-0.5*dt, t+0.5*dt or estimated at time t? If gmx3.3 uses leap-frog form of verlet, velocites at time t ar

Re: [gmx-users] protein problem

David van der Spoel wrote: Original Message Date: Mon, 12 Jun 2006 16:47:11 +0100 From: Didier Mu-kindemb <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi David, My name is Didier and I am a Bioinformatics student at Oxford university. I am writing to seek help with Gromacs. I

[gmx-users] protein problem

Original Message Date: Mon, 12 Jun 2006 16:47:11 +0100 From: Didier Mu-kindemb <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi David, My name is Didier and I am a Bioinformatics student at Oxford university. I am writing to seek help with Gromacs. I am doing a molecular dynam

Re: [gmx-users] QM method or basisset (CPMD) is not implemented

Hi Mahnam, This error message is delivered by Gromacs. There could be either of the two possibilities: 1) either you have compiled the official Gromacs-3.3 or 3.3.1 which does not yet contain the CPMD-related modifications (I guess, this is not the case), or 2) you have downloaded the righ

Re: [gmx-users] special molecule

Hi, On Monday 12 June 2006 17:25, Dongsheng Zhang wrote: > Sear Mark, > > Since PRODRG server only generates a itp file by using gromos type force > field, do I have to use gromos force field for my whole protein-ligand > system if my ligand force field parameters are got from PRODRG? In > another

Re: [gmx-users] special molecule

So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?On 6/12/06, Alan Dodd <[EMAIL PROTECTED]> wrote:It's entirely possible to mix and match forcefield files to create a hybrid forcefield - the lipidforcefield I use

Re: [gmx-users] special molecule

It's entirely possible to mix and match forcefield files to create a hybrid forcefield - the lipid forcefield I use has OPLS parameters for the headgroups, custom parameters for lipid tails, and GMX parameters for everything else. As long as the hybrid forcefield is internally consistent, it will

Re: [gmx-users] grompp error:Invalid order for directive defaults

Hi, I don't think you can use two force fields at the same time, and I think this would be a bad idea even if you could. That is, force fields are parameterized to work well with themselves, NOT with other force fields. That's why, for example, you don't model, say, the alpha helical part of a pr

Re: [gmx-users] grompp error:Invalid order for directive defaults

Dear David, Thank you for your help. It makes sense now. However, it leads me to ask you another question: My poly.itp is got from PRODRG server. It has gromos type force field paramters. Do you think my cnt.itp has to be gromos type force field format as well (atomtype, bondtype etc)? In fact I

Re: [gmx-users] special molecule

Sear Mark, Since PRODRG server only generates a itp file by using gromos type force field, do I have to use gromos force field for my whole protein-ligand system if my ligand force field parameters are got from PRODRG? In another word, can I mix two different force field (one for protein, one for

Re: [gmx-users] grompp error:Invalid order for directive defaults

Dongsheng Zhang wrote: Dear David, Thank you very much for your reply. I am sorry to tell you that I get the same error mesasge after I try your suggestion. Any other suggestion? check the manual, check the archives. you can not have two defaults sections. I think the question is if we ca

Re: [gmx-users] special molecule

I think you can use editconf to convert your original pdb to a gro file. On Mon, 2006-06-12 at 13:48 +, Tamas Horvath wrote: > As I understand, if there are "special" molecules in a pdb file, > pdb2gmx cannot convert it. However, PRODRG can create an *.itp file > for that molecule, so that I

Re: [gmx-users] special molecule

Tamas Horvath wrote: As I understand, if there are "special" molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or ev

Re: [gmx-users] grompp error:Invalid order for directive defaults

Dear David, Thank you very much for your reply. I am sorry to tell you that I get the same error mesasge after I try your suggestion. Any other suggestion? I think the question is if we can put two sets of force field parameters in two itp files which will be included in one topology file. From

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

well, i have installed the rpm versions of gromacs, and gromacs-mpi, didn't compiled it by hand. i just wonder if there is an example of using gromacs with mpi, like the demo in /usr/share/gromacs/tutor/demo but showing the usage with mpi. ThanksOn 6/12/06, kobi <[EMAIL PROTECTED]> wrote: Oh, thank

[gmx-users] special molecule

As I understand, if there are "special" molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I conv

[gmx-users] Langevin dynamics question

Hi, I would appreciate some advice on running Langevin dynamics in GROMACS. I plan to do a coarse-grained simulation in vacuo (ie 4 'atoms' to 1 particle) and was wondering what sort of value to use for the frictional term? I'm guessing that as each particle is heavier than in atomistic simulation

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Oh, thanks for correction. I'm sorry I got the exact details wrong. Didn't want to confuse anyone. Jan Mark Abraham schrieb: > kobi wrote: >> Hi Francisco >> >> If you intalled gromacs-mpi directly, then try to use just mdrun instead >> of mdrun_mpi. Normally you only have a mdrun_mpi if the >> s

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

kobi wrote: Hi Francisco If you intalled gromacs-mpi directly, then try to use just mdrun instead of mdrun_mpi. Normally you only have a mdrun_mpi if the singleprocessorversion was installed first and you only added the multiprocessorversion afterwards. Not strictly true. You need mdrun_mpi fo

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Hi Francisco If you intalled gromacs-mpi directly, then try to use just mdrun instead of mdrun_mpi. Normally you only have a mdrun_mpi if the singleprocessorversion was installed first and you only added the multiprocessorversion afterwards. ciao Jan Francisco Tufró schrieb: > David, thanks for

[gmx-users] re:grompp error:Invalid order for directive defaults

  It may caused by the difference in file type of top . Did you change your top file under win system. If yes , you should change it to unix type. Also you can check the property of top file.   祝   好   *Ji Qing（吉青）Institute of Chem

Re: [gmx-users] Adding hydrogen

Sheng Yong yang wrote: Hi, Dear Gromacs Users, Seems pdb2gmx just can add hydrogen to the main chain, not side chain (one can check the tutor demo file). I wonder whether it is not necessary to add hydrogen on the side chain in Gromacs or one has to add the side chain hydrogen by other software.

Re: [gmx-users] grompp error:Invalid order for directive defaults

Dongsheng Zhang wrote: Dear GMX users, I'd like to study the interaction between carbon nanotube and a polymer chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files contains force field parameters (such as [ defaults ], [ atomtypes], [ bondtypes ]), in this way, I don't need t

Re: [gmx-users] Shutting down in Windows2000

raja wrote: Thanks Mark for your reply, I run MD for 100 (2ns) at dt = 0.002. In both occasion, shutdown happened during mid night at around 7800 steps. I could not fix the problem by looking at log file as it does not contain any information regarding this. Is it possible that the gromacs