Re: [gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

On 5/21/16 9:47 AM, Antara mazumdar wrote: Dear Sir, The MD.trr i expect to be having 382ns of data as is mentioned in the log file and MD.xtc that was generated alongwith MD.trr when the simulation ran has 382ns. However, MD.trr has problems in giving output beyond 25ns. Could it be

[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

Dear Sir, The MD.trr i expect to be having 382ns of data as is mentioned in the log file and MD.xtc that was generated alongwith MD.trr when the simulation ran has 382ns. However, MD.trr has problems in giving output beyond 25ns. Could it be corruption of frames or something? Kind Regards,

Re: [gmx-users] Protein-membrane simulation error.

On 5/20/16 6:28 PM, BIJENDRA KHADKA wrote: Hello, I received the following error while trying to run "Adding ion" step during Protein-membrane simulation. Any advice or suggestions will be greatly appreciated. You need to tell us all the steps you have taken prior to this point, otherwise

Re: [gmx-users] help required in plotting percentage of protein in contact with membrane vs time

On 5/21/16 8:54 AM, Antara mazumdar wrote: Dear Gromacs users, I have a membrane protein simulation performed with gromacs 4.6. I have calculated the minimum distance of protein residues from upper leaflet of the lipid bilayer. I also have the time wise atom pair contacts as an output. The

[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

Dear Gromacs users, I have a membrane protein simulation performed with gromacs 4.6. I have calculated the minimum distance of protein residues from upper leaflet of the lipid bilayer. I also have the time wise atom pair contacts as an output. The following command i used : g_mindist -f

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So don't use -dump at all. You'll only get one frame though, using a spacing of 1 ns. Cheers, Tsjerk On May 21, 2016 13:53, "Tsjerk Wassenaar" wrote: > Hi Antara, > > You indicate you want the frame at

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Hi Antara, You indicate you want the frame at 27ns (-dump 27000), but that's not in the trajectory. The suggestion is to ask for a frame that is in, like -dump 25290 Cheers, Tsjerk On May 21, 2016 13:09, "Antara mazumdar" wrote: Dear gromacs users, I was trying to

[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Dear gromacs users, I was trying to dump structures from MD.trr using trjconv. The MD.trr has 0ns to 382ns of data. (i checked the MD.log file also). However, when i try to dump structures beyond 25ns, with the following command : *gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr