[gmx-users] electric field

Dear users, I applied electric fields of different magnitudes (less than 1 v/nm since higher amounts are avoided) in my system. I have some charged water molecules and I expected to see very different results when the magnitude is changed, but haven't got that much difference. How can I be sure

Re: [gmx-users] Problems with trjconv

Hi, Certainly. You do not want to convert non-trivial trajectories to text format. Mark On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña wrote: > well, I check and it is the same line of command. The biggest file has > more weight than the .traj file and it is only a .gro

[gmx-users] Problems with trjconv

Hello, I have a question about trjconv. I have a .trr file and I put the following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and got a file of 506444 bytes. Do you know what is happening?Mishelle

Re: [gmx-users] Problems with trjconv

Eh, I don´t understand what you mean, please explain me .Mishelle:) > From: mark.j.abra...@gmail.com > Date: Sun, 15 Nov 2015 19:28:47 + > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problems with trjconv > > Hi, > > Certainly. You do not want to convert non-trivial trajectories

Re: [gmx-users] restart issues with Gromacs

Hi, GROMACS assumes the file systems actually write to disk when you use the system call that means that, and works correctly if so. But if the file system or its configuration don't actually do that (for "performance" or erroneous reasons), then all bets are off. mdrun can't even know if it's

Re: [gmx-users] Problems with trjconv

Ok, but this erase the frame from my trajectory? because i don´t want to modify it. > Date: Mon, 16 Nov 2015 00:10:07 +0100 > From: shantanu...@gmail.com > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problems with trjconv > > If you want to take out only one frame then you can use

Re: [gmx-users] restart issues with Gromacs

Thanks Mark, Ok, so it sounds very much like it¹s on the cluster side. I¹ll fire this across to one of the sys admins and see if they can find out what the problem is, although I have no idea what and if they will find anything. >From the looks of it, the reading of the checkpoint file data was

Re: [gmx-users] Problems with trjconv

Yes, but I am not converting all the .trr file to gro I wanted to take only one frame of the .trr and make it gro. That´s why my command is trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro if the command line above is wrong :( what is the command I should use for taking out only one

Re: [gmx-users] Problems with trjconv

No it will not erase anything from .trr file. On Mon, Nov 16, 2015 at 12:21 AM, Mishelle Oña wrote: > Ok, but this erase the frame from my trajectory? because i don´t want to > modify it. > > > Date: Mon, 16 Nov 2015 00:10:07 +0100 > > From: shantanu...@gmail.com > > To:

Re: [gmx-users] Problems with trjconv

Hi, Your question had one-word answer, which I gave! :-) If the size of your files is worth thinking about, then converting them to gro format is not a great idea. Mark On Sun, 15 Nov 2015 21:56 Mishelle Oña wrote: > Eh, I don´t understand what you mean, please

[gmx-users] Choosing LINCS setting / rcon for parallel mdrun

Dear Users, I tried to do a NVT run on a cluster with -np = 64. My system size is 12405 atoms ( a protein in water ) I get the following error. ERROR. There is no domain decomposition for 56 nodes that is compatible with the given box and a minimum cell size of 0.959375 nm Change the number of

Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun

On 11/15/15 8:09 PM, Agnivo Gosai wrote: Dear Users, I tried to do a NVT run on a cluster with -np = 64. My system size is 12405 atoms ( a protein in water ) I get the following error. ERROR. There is no domain decomposition for 56 nodes that is compatible with the given box and a minimum

[gmx-users] difference between entropic energy and free energy

Deer list, I am quite confused about the concept of entropic energy and free energy. Could anybody help to tell me what is the difference between them? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] (no subject)

Dear gromacs users, Does anybody have an idea about the value of isothermal compressibility at kbar pressures. yours, Mehriar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Problem with GROMACS simulation

Dear Shantanu, As Erik already told you, your attachments aren't accepted by the list so nobody can see them. You need to download your files to some public place where everyone can access them if they want, e.g. Dropbox, etc. Without looking at the relevant files, nobody can possibly help your

Re: [gmx-users] Problem with GROMACS simulation

How do i get help regarding my simulations? I am working on an alkane system using TraPPE force field. There is some issue which I can't figure out how to solve. On Sat, Nov 14, 2015 at 9:54 PM, Erik Marklund wrote: > Hi, > > I don’t think attachments are

[gmx-users] gmx-us...@gromacs.org

Hello, I have a question about trjconv. I have a .trr file and I put the following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and got a file of 506444 bytes. Do you know what is happening? Mishelle

Re: [gmx-users] Problems with trjconv

Hi, Either you didn't issue the same command (inspect your terminal history), or the second operation didn't complete (for any number of reasons). Mark On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña wrote: > Hello, I have a question about trjconv. I have a .trr file and I

Re: [gmx-users] Problems with trjconv

well, I check and it is the same line of command. The biggest file has more weight than the .traj file and it is only a .gro file . Is this posible? Mishelle > From: mark.j.abra...@gmail.com > Date: Sun, 15 Nov 2015 19:15:50 + > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problems