Re: [gmx-users] Problem with running crystal simulation

Hello, Ben. Looks like your box blew up [ http://www.gromacs.org/Documentation/Terminology/Blowing_Up ]. It would be useful to know the initial box size and how well the minimization converged (were the forces low enough? How was the box pressure?). Are you sure the box size is adequate for your

Re: [gmx-users] Backmapping of POPE

Hi Ganesh, Can you send me the coarse grained structure and the atomistic topology (off-list)? Cheers, Tsjerk On Nov 23, 2015 20:46, "Ganesh Shahane" wrote: > Dear Gromacs users, > > I have a mixed POPE:POPG bilayer in Martini ff which I wish to backmap into > Charmm36 ff. To that effect, I am

[gmx-users] Backmapping of POPE

Dear Gromacs users, I have a mixed POPE:POPG bilayer in Martini ff which I wish to backmap into Charmm36 ff. To that effect, I am using the script developed by Tsjerk. However, I am getting the following error, which terminates the process even before it starts: Problem determining mapping coordi

Re: [gmx-users] TIP3P for GROMOS96 force field

You may not want to use TIP3P with GROMOS ffs, as the latter were intended/developed to be used with the SPC variants. Still, if you really want to use TIP3P, you'll have to get your hands dirty and let the force field know about the water model in question. I.e. you must edit the force field. A f

[gmx-users] TIP3P for GROMOS96 force field

Dear Gromacs users, I am going to use TIP3P water model in GROMOS96 54a7 force field. But in water model selecting menu, there are only SPC and SPCE suggestions. How can I add TIP3P to GROMOS96 54a7 force field? In directory of gromos54a7.ff, there is a tip3p.itp file. When I use it, error "Atomty

[gmx-users] Problem with running crystal simulation

Dear GROMACS user, I have a problem here when I am trying to run a crystal simulation, this is the warning I am getting from the error file: Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3):

Re: [gmx-users] symtab get_symtab_handle error

Dear Justin, Thanks for your reply. For several reasons I'd like to do the rest of the simulations with Gromacs 5.0. I read on the previous posts that one solution to avoid this problem would be to extend the simulation using grompp. Following that gives really strange results: I generated the tpr

Re: [gmx-users] support mmcif format?

Hi, Indeed, that does make more sense. It's conceivable we'd add such support for the next version (since if we can read it by bundling some code from RCSB, then maybe writing will be straightforward). Multiple users being interested in such support would make that more likely :-) Mark On Mon, N

Re: [gmx-users] How can I split .xtc file to two part?

Le 23/11/2015 15:56, Hassan Aaryapour a écrit : for resolving this problem, can I split .xtc file to two part? how? Dear Hassan, Except if you have a specific interest in water molecules, you should probably reduce your system to the molecule of interest by doing a subselection of it (only the

Re: [gmx-users] H-REMD in umbrella sampling

One can make two virtual particles at COMs of corresponding molecules and set harmonic potential between them with different length for lambdas 0 and 1. -- Best regards, Yuri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

Re: [gmx-users] How can I split .xtc file to two part?

On 11/23/15 9:56 AM, Hassan Aaryapour wrote: Dear Gromacs Users How can I make a movie from gromacs trajectory file (200 ns)? VMD was failed because of low memory of computer (16GB). for resolving this problem, can I split .xtc file to two part? how? gmx trjconv -b -e -Justin -- ==

[gmx-users] How can I split .xtc file to two part?

Dear Gromacs Users How can I make a movie from gromacs trajectory file (200 ns)? VMD was failed because of low memory of computer (16GB). for resolving this problem, can I split .xtc file to two part? how? Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gro

Re: [gmx-users] support mmcif format?

probably there is some misunderstanding. I didn't mean to store Gromacs trajectory to mmCIF format, but extracting a specific snapshot from Gromacs trajectory into mmCIF file. It is no doubt that the .xtc or .tng format is the best format for Gromacs trajectory. However, when we use command:

Re: [gmx-users] support mmcif format?

Hi, On Mon, Nov 23, 2015 at 12:09 PM Hannes Loeffler wrote: > On Mon, 23 Nov 2015 09:57:55 + > Mark Abraham wrote: > > > I think we are unlikely to plan to write mmCIF directly as a > > trajectory format, > > It's hard to see for me why someone would even want to use mmCIF as > a trajector

Re: [gmx-users] support mmcif format?

On Mon, 23 Nov 2015 09:57:55 + Mark Abraham wrote: > I think we are unlikely to plan to write mmCIF directly as a > trajectory format, It's hard to see for me why someone would even want to use mmCIF as a trajectory format. The format serves, primarily, the crystallography community to stor

Re: [gmx-users] support mmcif format?

Hi Mark: thanks a lot for such explanations. I really looking forward to that Gromacs will one day support exporting trajectory to mmCIF format. The current .PDB format really cost plenty of problems due to its limitation, especially considering nowadays simulations system become bigger and b

[gmx-users] H-REMD in umbrella sampling

Hi, I posted a question about Hamiltonian REMD in umbrella sampling simulations on 20.11.2015 but haven't got any answer yet. In the meantime I found a topic on gromacs redmine which is related to my post: http://redmine.gromacs.org/issues/1335. May I ask what is the current status of the suppo

Re: [gmx-users] support mmcif format?

Hi, We've talked about this internally once or twice, but nobody's taken action. We should probably add support for reading it. IIRC there's some code available already we might import. I think we are unlikely to plan to write mmCIF directly as a trajectory format, in that we already have prelimin