Re: [gmx-users] Re: choice of force field -reg

Dear Sir, Thank you so much for the response. Revathi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe request

[gmx-users] Vritual Sites and simulation time-step

Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. >From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce numb

[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? >From my understanding there should not be, since there are no charges which >treatment you use shouldn't' make a difference. However, it does and I am trying to work out wh

[gmx-users] .GRO Formatting

I'm working on a .GRO file and have come across a formatting error. In the manual, it states that the spacing for each column in the .GRO file is: residue number (5 positions, integer) residue name (5 characters) atom name (5 characters) atom number (5 positions, integer) position (in nm, x

Re: [gmx-users] pulling simulations

On 5/29/13 9:19 AM, Sathish Kumar wrote: Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. There is no systematic way to set these values, at least none that I know of. Everyone has their own impression of wha

Re: [gmx-users] Extending simualtions

If you want to have the default behaviour of appending new output to the old files, GROMACS needs to be able to find those files and their content must be unchanged. If you cannot/will not satisfy that condition, you can use mdrun -noappend to force GROMACS to simulate on. Making sense of your outp

[gmx-users] Re: Extending simulations

perhaps mdrun -cpi -deffnm full will also do the job in your case On Wed, May 29, 2013 at 6:36 PM, Dr. Vitaly Chaban wrote: > I do not remember all the keys. > > Rename your files to their default names and you will have nothing to > specify except > > mdrun -cpi > > > > > On Wed, May 29, 2013

[gmx-users] Re: Extending simulations

I do not remember all the keys. Rename your files to their default names and you will have nothing to specify except mdrun -cpi On Wed, May 29, 2013 at 6:31 PM, Fábio Filippi Matioli < fabiof...@hotmail.com> wrote: > Hello, i'm who asked about extending simulations. > You sad for me pen teh

RE: [gmx-users] g_covar -ascii

Hello, I am interested in dynamical analysis of my protein. In the manual, it says -ascii generates a file that includes the whole covariance matrix, and -xpma writes the atomic covariance matrix per pair of atoms. I was wondering if there is a way to have this atomic covariaces in the .dat file wi

Re: [gmx-users] pulling simulations

The force should not probably exceed kT product too much... Dr. Vitaly Chaban On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar wrote: > Dear Sir, > In pulling simulations how to set pull_rate and > pull_k .On which basis we can set these values. > -- > regards > M.Sathish

Re: [gmx-users] Extending simualtions

On Wed, May 29, 2013 at 3:14 PM, Fábio Filippi Matioli < fabiof...@hotmail.com> wrote: > Hello, I have a problem. > I try to extending my simulation. I made this steps. > > tpbconv -s previous.tpr -extend timetoextendby -o next.tpr > mdrun -s next.tpr -cpi previous.cpt > > I need to put more thing

Re: [gmx-users] How to choose bd_fric value in brownian dynamics

Hello Mohan - I do not use Brownian dynamics code routinely to have exact values for various cases, but if I were you, I would start with smaller value and then increase, until your simulation runs fine. The time-step depends not on the method, but on characteristic oscillations (bond lengths, etc

Re: [gmx-users] How to choose bd_fric value in brownian dynamics

Hello Sir , Thanks for your quick reply. I have used bd_fric =0 and then my simulation is blowing up. I have used a time step of 0.002ps, Hence i thought if i can use some other value rather than zero but I do not know which value to use. Can you suggest any general value for protein wa

[gmx-users] pulling simulations

Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http:

[gmx-users] (no subject)

Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http:

[gmx-users] Extending simualtions

Hello, I have a problem. I try to extending my simulation. I made this steps. tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I need to put more things on mdrun, or only this? because my first mdrun had 4 or 5 outputs, or the extending recognize de

[gmx-users] GBSA problem

Dear gmxusers, I am using gromacs version 4.5.4 and i am simulating a surface upon base pairs on it. I would like perform simulation with the GBSA implicit solvent model and I have tried that but one problem occurs during running. Actually grompp has having some problem with the r

Re: [gmx-users] How to choose bd_fric value in brownian dynamics

According to my understanding, setting friction coefficient is quite a personal thing. The higher is bd-fric, the smaller are velocities. Why not to set bd-fric = 0 in order to start with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Moh

[gmx-users] Re: choice of force field -reg

If you want to observe H-bond dynamics and do it with an atomistic precision than, of course, you need an all-atom representation. United atoms will still *effectively* account for H-bonding, if you are happy with reduced precision. Dr. Vitaly Chaban On Wed, May 29, 2013 at 8:01 AM, Revthi San

Re: [gmx-users] Continue simulation from the specific time

Thanks! 2013/5/29 Dr. Vitaly Chaban > If the frame was saved to the trajectory file, just extract it with > > trjconv -dump $timeframe -o conf.gro > > and continue your MD. > > No need for any additional energy minimizations, of course. > > Dr. Vitaly Chaban > > > > > > > On Wed, May 29, 2013 a

Re: [gmx-users] Continue simulation from the specific time

Aside from original question, you will probably want to initialize velocities (gen_vel) in order to evolve a different trajectory rather than repeating previous one. Dr. Vitaly Chaban On Wed, May 29, 2013 at 1:00 PM, Dr. Vitaly Chaban wrote: > If the frame was saved to the trajectory file,

Re: [gmx-users] Continue simulation from the specific time

If the frame was saved to the trajectory file, just extract it with trjconv -dump $timeframe -o conf.gro and continue your MD. No need for any additional energy minimizations, of course. Dr. Vitaly Chaban On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар wrote: > Hello, I've got a questio

[gmx-users] Continue simulation from the specific time

Hello, I've got a question. Is there a way to continue MD simulation, not from last state but from specific time of MD? Say we have made a MD, have analysed it and have found an interresting molecule conformation at specific frame. Can we continue from this point or we should extract this frame, ma

[gmx-users] How to choose bd_fric value in brownian dynamics

Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. M