Re: [gmx-users] doing restarts

Juliette N. wrote: On 10 September 2011 18:03, Justin A. Lemkul > wrote: Juliette N. wrote: Hello, I am trying to extend a simulation to 2 ns and wanted to know if I am using the proper tools for this purpose. (version 4.5.4)

Re: [gmx-users] doing restarts

On 10 September 2011 18:03, Justin A. Lemkul wrote: > > > Juliette N. wrote: > >> Hello, >> >> I am trying to extend a simulation to 2 ns and wanted to know if I am >> using the proper tools for this purpose. (version 4.5.4) >> >> 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -unt

Re: [gmx-users] doing restarts

Juliette N. wrote: Hello, I am trying to extend a simulation to 2 ns and wanted to know if I am using the proper tools for this purpose. (version 4.5.4) 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000 mdrun -s old-extend.tpr -cpi old.cpt -o old-extend -c old-e

[gmx-users] doing restarts

Hello, I am trying to extend a simulation to 2 ns and wanted to know if I am using the proper tools for this purpose. (version 4.5.4) 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000 mdrun -s old-extend.tpr -cpi old.cpt -o old-extend -c old-extend -e old-extend Is

[gmx-users] MD Simulations

Dear friends, Please read nice article on MD Simulations http://www.springerlink.com/content/6jt0843463226321/ -- Pawan -- 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_Li

[gmx-users] comm_mode and accelerate

Dear all， To make molecules move, accelerate should be used. nstcomm is the frequency for center of mass motion removal But if they are used together, the molecule will not move. I made a model system: a box of pure water. Adding accelerate to SOL in Z direction. Firstly, comm_mode was set t

Re: [gmx-users] how to modify the md. log

On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul wrote: > > > lina wrote: > >> Hi, >> >> My job terminated due to the storage out of the quote given by >> administrator, >> >> here the md.log is unusual, so when I resume the job, the results won't >> append on it. but still running... >> >> Here

Re: [gmx-users] radial distribution function

On Sat, Sep 10, 2011 at 10:00 PM, Moeed wrote: > Thank you for your input. I am going to run for another 15 ns to see if the > little jumps vanish. > > Best, > > g_rdf -bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the ar

Re: [gmx-users] radial distribution function

Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish. Best, On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul wrote: > > > lina wrote: > > >> >> On Sat, Sep 10, 2011 at 3:35 AM, Moeed > lecielll@googlemail.**com >> wrote: >> >>Dear users, >> >>I

Re: [gmx-users] how to modify the md. log

lina wrote: Hi, My job terminated due to the storage out of the quote given by administrator, here the md.log is unusual, so when I resume the job, the results won't append on it. but still running... Here is the tail of md.log, DD step 31424999 load imb.: force 20.8% pme mesh/f

Re: [gmx-users] Re: gmx-users Digest, Vol 89, Issue 52

ers of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you -- *ó Í! *** * Nemo me impune lacessit* -- next part -- An HTML attachment was scrubbed... URL: http://lists.g

Re: [gmx-users] Representative structure from MD trajectories

Sir, thanks for your reply Yes I should have limited number of structure for a given point(pc1,pc2) but in my case, I have taken pc1 and pc2 as a range of points where the minima in FEL lies rather than a single point.So I think it would be relevant to apply the clustering as per your suggestio

[gmx-users] Re: how to modify the md. log

On Sat, Sep 10, 2011 at 5:05 PM, lina wrote: > Hi, > > My job terminated due to the storage out of the quote given by > administrator, > > here the md.log is unusual, so when I resume the job, the results won't > append on it. but still running... > > Here is the tail of md.log, > > DD step

[gmx-users] how to modify the md. log

Hi, My job terminated due to the storage out of the quote given by administrator, here the md.log is unusual, so when I resume the job, the results won't append on it. but still running... Here is the tail of md.log, DD step 31424999 load imb.: force 20.8% pme mesh/force 1.936

Re: [gmx-users] Representative structure from MD trajectories

Hi Bipin, The averages from (2) and (3) are the same and may be far from realistic. Minimizing an average structure may not always yield a structure that is relevant or representative of the ensemble. I would suggest clustering But you should only have a limited number of structures for a given po

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52

parameters > of index file [all atoms within a sphere with a chosen radius around > selected atom]. What can i do? Thank you > > > -- > *ó Í! > > > *** > * > > Nemo me impune lacessit* > -- next part -- > An HT