Re: [gmx-users] High Temperature 498 K, NVT or NTP ?

Hi Lin, Not really surprising that water, even SPC, evaporates at 498K and 1 bar, right? (Assuming you performed the simulation at 1 bar). The expansion of the system with NVT seems unlikely, as the volume is fixed. If it really expands, you have pressure coupling turned on, and should double

[gmx-users] multiple torsions for one dihedral

Hi all, I'm using AMBER99p force field in GROMACS. In the AMBER forcefield for some dihedrals, there are several values, in which n values are different.  As an example, for C3-C3-N-C, I have C3-C3-N-C   .50  180.0  -4 C3-C3-N-C   .15  180.0  -3 C3-C3-N-C   .53  0.0   1 For the version 4,

[gmx-users] Reg:walls and pbc xy

Hi Gromacians I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy

Re: [gmx-users] multiple torsions for one dihedral

Yes, multiple type 1 dihedrals for use with AMBER and CHARMM forcefields can be implemented, either as successive [dihedraltypes] of type 9 (since GROMACS 4.0, IIRC) or as multiple [dihedrals] of type 1 (since ages). Mark - Original Message - From: Amin Arabbagheri amin_a...@yahoo.com

[gmx-users] questions about umbrella sampling

Dear All: I am using umbrella sampling method to calculate potential of mean force and I encountered the following questions: 1, at the *.ppa file, I need to incorporate a parameter indicating the the position of the pull group will restraint to, relative to the reference group (i.e., the pos1

RE: [gmx-users] Reg:walls and pbc xy

Hi, With wall_r_linpot your wall potential is linear from 1 nm downwards. Since the LJ force is negative at 1 nm, your atoms are attracted to the walls. But why not simply use two interfaces? You get double the sampling for free and you do not have to bother with complicated wall setups. Berk

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk I need only one interface because if i have two interfaces the capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off (this was said in the literature). Can anyone explain me

[gmx-users] g_energy problem with 4.5.1 and 4.5.2

Hi everybody, I run NPT simulations (with the double precision version of mdrun) of a polymer melt with anisotropic pressure scaling The simulation seems to go fine, and the trajectories look reasonable, but there's something wrong with my g_energy output. === With 4.5.1 I get weird values

RE: [gmx-users] Reg:walls and pbc xy

Hi, I have not heard about such issues, but it might depend a lot on your particular application. I would think you will always have disturbances, no matter if you use two interfaces, one interface with walls or one liquid-liquid interface and two liquid-vapour interfaces. The only solution

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk Thank you once again. How can i use thick layers and what is the procedure? can you explain it bit more on this? Regards Vinoth On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess g...@hotmail.com wrote: Hi, I have not heard about such issues, but it might depend a lot on your particular

RE: [gmx-users] Reg:walls and pbc xy

I meant to say that if you see effects of one interface on another with a layer of 1 nm thickness/height, these effects will be less with a layer of 2 nm thickness and even less with 10 nm thickness. Berk Date: Tue, 2 Nov 2010 15:30:34 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From:

[gmx-users] Re: Charmm36 FF and membrane

As I said please keep all correspondence on the GROMACS mailing list for general GROMACS problems. You can use genconf to increase the size of the membrane. Cheers Tom tusar ban wrote: Thanks for your reply. The link that you have suggested contains the POPE structure. However that is too

[gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/9d1f3ca5

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk Thank you. what settings i should change in mdp file (energy minimisation) to run the energy minimisation for the single liquid-liquid interface (liquid-vapour interface at the other two extremes) without any issues? kindly be specific ( what parameter i should change) below is my mdp

Re: [gmx-users] g_energy problem with 4.5.1 and 4.5.2

Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. Sander On 2 Nov 2010, at 10:28 , Michael Brunsteiner wrote: Hi everybody, I run NPT simulations (with the double precision version of mdrun) of a polymer melt with anisotropic pressure scaling The

[gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

Sander pronk wrote: Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. thanks for your swift reply! I assume any fix will be in the Git version only for some time to come, right? cheers, Michael Sander -- gmx-users mailing list

Re: [gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8

/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/9d1f3ca5/attachment

RE: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

Well, it seems that any double precision energy file can not be read by 4.5.1 or 4.5.2 code. This is such a serious issue that we should bring out 4.5.3 within a week. If you only need the box, g_traj can produce that. If you need other energies you can use a 4.5.1 g_energy for the moment.

Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

Hi Michael, I've just committed a fix to the git repository (it's in the release-4-5-patches branch) There were 2 problems - Energy files in double precision couldn't be read in 4.5.2, due to an overly strict error checking issue. - The box matrix wasn't written out correctly (in any 4.5

[gmx-users] Update: (Problem Solved) -- Job crash: checkpoint file

Thanks to our HPC support team who solved my problem. They did something to my account and now I am able to run large replica exchange jobs. I don't know whether this is really related to disk quota or special permission. But for anyone who encountered this type of problem, you can try running

[gmx-users] (no subject)

Dear gmx-users, I have a rather elementary question regarding the value of box vectors when invoked by g_energy. If I am shearing a system using deform option, what does exactly, say, Box-XY represent? Thanks, gc -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_hbond

Hi to all, I'm sorry I'm asking again a question I asked a week ago but I still haven't found my answer: I concatenated 3 trajectories of 3 different molecules (that have the same number of atoms) with trjcat: trjcat -settime Then I ran g_hbond on the concatenated trajectory, I got an index.ndx

[gmx-users] Principal axis (g_principal)

Dear Sarah, I just ran into the same thing so I'm posting this as a very late response to your querry. I think that g_principal prints the transpose of the principal axes matrix, which is the exact opposite of what one would expect. (1) First, I define a system that is longest in Z,

[gmx-users] pressure of the liquid in NPT and NVT

Hi all, Please suggest me what is the reason for the below situation. The 1728 TIP4P waters system was simulated in NPT under 1bar maintained with Parrinello-Rahman barostat at 300K. Some results are below: Energy Average RMSD Fluct. Drift Tot-Drift

Re: [gmx-users] g_hbond

Carla Jamous skrev 2010-11-02 17.35: Hi to all, I'm sorry I'm asking again a question I asked a week ago but I still haven't found my answer: I concatenated 3 trajectories of 3 different molecules (that have the same number of atoms) with trjcat: trjcat -settime Then I ran g_hbond on the

Re: [gmx-users] g_hbond

Erik Marklund skrev 2010-11-02 20.33: Carla Jamous skrev 2010-11-02 17.35: Hi to all, I'm sorry I'm asking again a question I asked a week ago but I still haven't found my answer: I concatenated 3 trajectories of 3 different molecules (that have the same number of atoms) with trjcat:

Re: [gmx-users] pressure of the liquid in NPT and NVT

- Original Message - From: Vitaly Chaban vvcha...@gmail.com Date: Wednesday, November 3, 2010 6:10 Subject: [gmx-users] pressure of the liquid in NPT and NVT To: gmx-users@gromacs.org Hi all, Please suggest me what is the reason for the below situation. The 1728 TIP4P waters

[gmx-users] Re: pressure of the liquid in NPT and NVT

Unless the box was equilibrated at NPT at the start of the NPT run, or the run was very long, the average value over the whole run is not all that likely to be one from the equilibrium range. Take the last frame. The system is pretty equilibrated. Just look at the energy drift - it is

RE: [gmx-users] Re: pressure of the liquid in NPT and NVT

What is the volume fluctuation like just prior to the end of the previous run (NPT) that is used as the starting point for the NVT run? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC

Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

Hi, On 11/2/10 1:35 PM, Sander Pronk wrote: Hi Michael, I've just committed a fix to the git repository (it's in the release-4-5-patches branch) There were 2 problems - Energy files in double precision couldn't be read in 4.5.2, due to an overly strict error checking issue. - The box matrix

[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

Hi I read some papers and many simulations were performed under high temperature to induce the unfolded protein. However, the authors did not mention how they conducted the simulations under high temperature, 498 K. They did not mention which NVT or NPT were adopted for such high temperature. None

[gmx-users] rotate a .xtc file?

Dear users, I have 100 GB of .xtc with 3E6 total frames that that I would like to rotate by 90 deg about the z axis. For a .gro file, I could do this with editconf. trjconv does not appear to have this ability. Writing out so many frames as .gro just to rotate it with editconf and turn

Re: [gmx-users] rotate a .xtc file?

Hi, since this is such a simple problem I suggest to simply write a program to do it. I suggest to start with either the xdrfile library or with the the template (available under share). My experience is writing those small things myself is much faster than searching the net and asking on the

Re: [gmx-users] Reg:walls and pbc xy

Hi all Can anyone help me out with the wall settings for running above mentioned liquid-liquid interface. with the mdp file i have my system is exploding. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote: Hi