Re: [gmx-users] Regarding TCoupling and position restraints

Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul wrote: > > > On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: > >> Hi, >> I am trying to simulate nanotube (1156) with protein and water and I am >> usi

[gmx-users] generation of gro file

Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. Here the xyz coordinates are attached for 18-crown-6. Thank in advance. Regards New learner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] Regarding TCoupling and position restraints

On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for

Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

On 15 Aug 2013 15:27, "grita" wrote > In short, the sigma is the separation or the 'diameter'. True or False ??? Neither. The diameter of a particle is a meaningless concept here. You have a continuous potential, not a definite boundary. If you want your particles to *almost* never come closer

[gmx-users] Regarding TCoupling and position restraints

Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures usin

Re: [gmx-users] About Error in mdrun

On 8/16/13 11:51 AM, vidhya sankar wrote: Dear justin Thank you for your previous reply When i run the md in gromacs 4.6.2 with plumed1.3 Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto:

Re: [gmx-users] for help about reading xtc file

It can be done either way. Whether to do it is up to you. The compiler is obviously reporting that your attempt to duplicate the code wasn't far-reaching enough. I suggest that extending the interface in the header file to return the position, and also to seek to a given position is a much better a

Re: [gmx-users] Re: Hai friends (balu)

I suppose there would also be a way of passing do_dssp output on to make_ndx then you could use the index with g_hbond to count hbonds in each secondary structure element. Best wishes James > If the goal is to simply count the secondary structure, pass the dssp > output file through grep "__" dss

[gmx-users] Re: Hai friends (balu)

If the goal is to simply count the secondary structure, pass the dssp output file through grep "__" dssp_output.xpm | wc Fill in the dssp code for each secondary structure in the underline separately. Grep would extract all characters that fit that pattern and wc would count it. Hope that helps.

Re: [gmx-users] for help about reading xtc file

If the xdrfile library can't do what I want, writing out the frames is an alternative. I know that the MDAnalysis has modified the xdrfile library to do seeking xtc file. But it seems that they do a python wrapper. Thanks, YC On Aug 16, 2013, at 12:35 PM, Mark Abraham wrote: > That's only worth

Re: [gmx-users] for help about reading xtc file

That's only worth bothering with if you'll do that re-read several times. Is writing out the frame(s) of interest a better solution? Mark On Fri, Aug 16, 2013 at 6:25 PM, Xu, Yechuan wrote: > Yes, I realized that it is a opaque structure. > I just want to read a certain frame from the > xtc file

Re: [gmx-users] Hai friends

If you want the residues in a particular secondary structure, you can use do_dssp, see http://manual.gromacs.org/current/online/do_dssp.html . g_hbonds can calculate hydrogen bonds. To separate the h-bonds by secondary structure, I suppose some scripting is needed. 2013/8/16 balu > >

Re: [gmx-users] for help about reading xtc file

Yes, I realized that it is a opaque structure. I just want to read a certain frame from the xtc file. For example, last time I read the xtc file to a certain frame, I want to recorde the position and next time I can read the xtc file from there, not from beginning. Did anybody do that? Thanks, YC

[gmx-users] About Error in mdrun

Dear justin Thank you for your previous reply  When i run the md in gromacs 4.6.2 with plumed1.3   Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores   and the -pin option is set to auto: will not pin thread to cores.   This c

[gmx-users] Hai friends

Can anyone suggest me to calculate the number of alpha-, 3-10, pi-helical hydrogen bonds in protein using gromacs. Is there any particular commands in gromacs, please let me know... Thank you... -- View this message in context: http://

[gmx-users] Restart REMD

Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int

Re: [gmx-users] Restart REMD

Probably the same issue as http://redmine.gromacs.org/issues/1072, which is probably fixed if you update to 4.5.7. Mark On Fri, Aug 16, 2013 at 3:05 PM, Min Wu wrote: > Hi gmx-users > > > > I had an error as followed when I restart my REMD with commands: > > > > mpirun mdrun_mpi -multi 96 -deffn

Re: [gmx-users] LINCS Constraints - all-bonds or h-bonds?

I often use 4 fs with all-bonds and virtual sites, especially if lacking sampling is a greater source of error than the kinetic energy being slightly off. Erik On 15 Aug 2013, at 20:58, Michael Shirts wrote: > I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic > e

[gmx-users] Restart REMD

Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26

Re: [gmx-users] psf to tpr

No, it is not. But you can at least convert coordinates via VMD. If you want to use gromacs trajectory analysis tools, it is easier to convert NAMD trajectory to gromacs trajectory. Otherwise, I have no idea why one may need to jump between codes. Dr. Vitaly V. Chaban On Fri, Aug 16, 2013 at 10

Re: [gmx-users] psf to tpr

I doubt there's a useful script - there's too many details to even have a reliable psf-to-top converter. Google will know if anybody does! Mark On Fri, Aug 16, 2013 at 8:17 AM, Venkat Reddy wrote: > Dear All, > I would like to convert my NAMD psf file to GROMACS tpr file? First of all, > is it p

Re: [gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster

It's trying to run a test MPI mdrun (with -version -maxh 0.001) to check that things work, before you get error messages that confuse the issue with doing actual PME run testing. So maybe you need to sort out the run-time working directories to match. See what you need to do to run such an mdrun "b

Re: [gmx-users] for help about reading xtc file

On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan wrote: > Thank you for your reply. after I read the xdrfile.c, > > I changed the sentence as > pos=xdr_getpos((XDR*) (xtc->xdr)); > > like that in the file of xdrfile.c. I also copy the definition > for XDR and xdr_op to my own code. You can see those