Re: [gmx-users] Simple gas-phase minimization help

On 6/16/16 4:25 PM, Tarick E wrote: Hi Mark, Thanks for the reply. I have attempted to run this on Gromacs installed on a local machine as well as on a cluster. In either case, the simulations would not complete after being run for ~12 hours. I feel that there is an error in my mdp file but I

Re: [gmx-users] Simple gas-phase minimization help

Hi Mark, Thanks for the reply. I have attempted to run this on Gromacs installed on a local machine as well as on a cluster. In either case, the simulations would not complete after being run for ~12 hours. I feel that there is an error in my mdp file but I am not sure what it could be. I'm

Re: [gmx-users] Simple gas-phase minimization help

Hi, We can't help if all we have is the information "does not produce an output." I suggest doing tutorial material locally before you get involved with the complexity of a cluster. Mark On Thu, 16 Jun 2016 19:01 Tarick E wrote: > I have tried a number of edits to my

Re: [gmx-users] Dielectric Constant

Hi, These are all documented in the mdp sections. What isn't clear? Mark On Thu, 16 Jun 2016 18:06 Life Sciences Inc < contact.lifesciences@gmail.com> wrote: > Hi all > > Exactly in Gromacs what and where is Dielectric constant option , If for > example I have to run simulations to study

Re: [gmx-users] Checksum and .log error

Hi, Mdrun is reporting that your entire file can't be read, which likely means that something a out the filsystem or the way you are using it is broken. It doesn't look like a gromacs problem... Mark On Thu, 16 Jun 2016 18:54 ingram wrote: > Version 5.1.2 >

Re: [gmx-users] PMF steadily increasing

Thank you very much for your suggestions. I will check your individual remarks and provide feedback. 2016-06-15 19:01 GMT+02:00 Christopher Neale : > (1) Are the protein and peptide really never interacting at d=7 nm? I > presume you've got a peptide that would be

Re: [gmx-users] Basic Understanding about Gromacs C library

Writing your own analysis tool in template.c might not be the best solution either. You have to worry about things like pbc breaking and you in many cases need to write routines that already exist elsewhere. I suggest looking into standalone analysis kits such as http://loos.sourceforge.net/ or

[gmx-users] Basic Understanding about Gromacs C library

Greetings, List, I have a set of data that I used to analyze through VMD. As the set is quite heavy and there are many of them, using VMD was a bit cumbersome. So it has been decided that working in GROMACS would present benefits. The first step that I executed was to compile via CentOs terminal

Re: [gmx-users] Simple gas-phase minimization help

I have tried a number of edits to my minim.mdp file for minimization with no luck. I can generate a tpr without any errors and initiate a simulation via mdrun, but no matter what resources I allocate to it (on a supercomputer), I cannot produce an output. Here's my mdp file. I am trying to

Re: [gmx-users] Checksum and .log error

Version 5.1.2 md_golp_vacuo.log is only 207KB md_golp_vacuo.cpt is 97KB md_golp_vacuo.trr is 19MB Im not sure what you mean but the .cpt files were all read at the same time. Best Teresa On 2016-06-16 15:07, Mark Abraham wrote: Hi, What GROMACS version? How big is the file? What does your

[gmx-users] Dielectric Constant

Hi all Exactly in Gromacs what and where is Dielectric constant option , If for example I have to run simulations to study behavior of water around molecules, and I am using experimental value of SPC/E water model as 71 for Dielectric constant. But in my input file for gromacs where I will put

Re: [gmx-users] Checksum and .log error

Hi, What GROMACS version? How big is the file? What does your filesystem report for the access times for all the output files? A possible culprit would be a file that is greater than 2GB in size being accessed when that can't work. Mark On Thu, Jun 16, 2016 at 3:03 PM ingram

Re: [gmx-users] MDRUN crash

On 6/16/16 6:10 AM, Luca Banetta wrote: Dear gmx users, I am meeting a lot of problems launching a simulation with shell particles. The mdp file is ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define

[gmx-users] Checksum and .log error

Dear Grommunity, I recently ran a several simulations that stopped but had not finished. I tried to restart them using mpiexec -np 320 mdrun_mpi -v -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir simann1 simann2 simann3 simann4 simann5 simann6 simann7 simann8 simann9

Re: [gmx-users] pdb2gmx error

Hi, Why is your residue numbering and residue naming changing in mutually inconsistent ways? Mark On Thu, Jun 16, 2016 at 9:36 AM bharat gupta wrote: > Hi, > > I have been trying to build the toplogy for cellopentoase using the newly > derived parameters mentioned in

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, On Thu, Jun 16, 2016 at 12:24 PM Husen R wrote: > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham > wrote: > > > Hi, > > > > There's just nothing special about any node at run time. > > > > Your script looks like it is building GROMACS fresh each

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham wrote: > Hi, > > There's just nothing special about any node at run time. > > Your script looks like it is building GROMACS fresh each time - there's no > need to do that, which part of my script ? I always use this

[gmx-users] MDRUN crash

Dear gmx users, I am meeting a lot of problems launching a simulation with shell particles. The mdp file is ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, There's just nothing special about any node at run time. Your script looks like it is building GROMACS fresh each time - there's no need to do that, but the fact that the node name is showing up in the check that takes place when the checkpoint is read is not relevant to the problem. Mark

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham wrote: > Hi, > > On Thu, Jun 16, 2016 at 9:30 AM Husen R wrote: > > > Hi, > > > > Thank you for your reply ! > > > > md_test.xtc is exist and writable. > > > > OK, but it needs to be seen that way from the

Re: [gmx-users] pdb2gmx error

Hi, I have been trying to build the toplogy for cellopentoase using the newly derived parameters mentioned in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the gromacs website: http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar When I try to

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, On Thu, Jun 16, 2016 at 9:30 AM Husen R wrote: > Hi, > > Thank you for your reply ! > > md_test.xtc is exist and writable. > OK, but it needs to be seen that way from the set of compute nodes you are using, and organizing that is up to you and your job scheduler, etc. >

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, Thank you for your reply ! md_test.xtc is exist and writable. I tried to restart from checkpoint file by excluding other node than compute-node and it works. only '--exclude=compute-node' that produces this error. is this has the same issue with this thread ?

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, The stuff about different nodes or numbers of nodes doesn't matter - it's merely an advisory note from mdrun. mdrun failed when it tried to operate upon md_test.xtc, so perhaps you need to consider whether the file exists, is writable, etc. Mark On Thu, Jun 16, 2016 at 6:48 AM Husen R