[gmx-users] Restart corrupted run

Hi all, how can I restart a MD run that stopped before finishing the calculations? I know about the solution in previous versions of Gromacs, but now I'm working with Gromacs 5.1.2. Thank you in advance. Mehrnoosh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Remove bad waters

of diffusion of water into the >membrane can be physical (I think!) but too much suggests your model is >broken somehow. >Mark On Wed, Apr 20, 2016 at 4:09 PM, Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > hi all, > > I'm simulating membrane, and when I check

[gmx-users] Problem with running Gromacs v. 5

thank you for your response dear Mark :) Regards Mehrnoosh On Tue, Feb 16, 2016 at 12:24 PM, Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > Dear Gromacs users, > > I had to use newer version of Gromacs, so I install Gromacs 5.1.2 package. > During installati

[gmx-users] Problem with running Gromacs v. 5

Dear Gromacs users, I had to use newer version of Gromacs, so I install Gromacs 5.1.2 package. During installation I got no error. But I have serious problem with using it!! Since I always used older version of Gromacs that was somehow user friendlier!! My problem is how can I run gromacs from an

[gmx-users] pulling simulation

I see. Thank you dear Justin. Best regards, Mehrnoosh On Sat, Feb 13, 2016 at 6:54 PM, Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > Dear all, > > I'm trying to do umbrella sampling. But after running "perl distances.pl", > I get a "sum

[gmx-users] pulling simulation

Dear all, I'm trying to do umbrella sampling. But after running "perl distances.pl", I get a "summary_distances.dat file which has NO distances! Before, I get an error "pull reference distance for group 1 is negative" while I run grompp and then mdrun for pulling simulation. Below is my

[gmx-users] Fwd: OPLA

Dear all, what does "CD C in Trp" in OPLS atomtype list stand for? Thank you in advance Mehrnoosh -- ** Mehrnoosh Kh. Hazrati PhD Candidate of Physical Chemistry,Tarbiat Modares University,Tehran, Iran *** Phone

[gmx-users] Fatal error: No molecule were defined in the system

Dear all, hi, I'm simulating the drug "5-Flouorouracil", since its topology file is not available, I've written it by hand. But I got the error "No molecule were defined in the system" when run grompp. where could be the problem? Thank you in advance. Regards, Mehrnoosh The .itp file is

[gmx-users] itp file - number of function

Dear all, hi in the case of writing the .itp file, is it correct to use different functions type for dihedrals?! Thanks you in advance Best Regards Mehrnoosh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Force constant

Dear all, I have to write the .itp file for my molecule, and I have problem with finding the correct value for force constants. Is it possible to calculate bond/angle force constant from ab initio calculation? Thank you in advance Mehrnoosh -- Gromacs Users mailing list * Please search the

[gmx-users] getting .gro file

Dear Gromacs users, I've already have the .pdb and .itp files for my structure. And I've written the .top file. How can I produce the .gro file for my structure? Thank you in advance Mehrnoosh -- Gromacs Users mailing list * Please search the archive at