[gmx-users] remove cemter of mass motion in particular direction

Dear Gromacs experts, Does anyone know if there is a way to remove center of mass motion in particular direction(s) only? Actually, I would like to remove system COM movements in X and Y directions only, while letting the system move as it likes in Z direction. As far as I can understand

[gmx-users] POPC with CHARMM

Dear Users, I want to simulate POPC membrane with CHARMM ff using GROMACS 4.6.5. but in CHARMM ff directory, there is no popc itp file. How can I proceed? Best, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] remove cemter of mass motion in particular direction

On 11/24/14 3:00 AM, Mikhail Stukan wrote: Dear Gromacs experts, Does anyone know if there is a way to remove center of mass motion in particular direction(s) only? Actually, I would like to remove system COM movements in X and Y directions only, while letting the system move as it likes

Re: [gmx-users] POPC with CHARMM

On 11/24/14 3:13 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I want to simulate POPC membrane with CHARMM ff using GROMACS 4.6.5. but in CHARMM ff directory, there is no popc itp file. How can I proceed? Download the CHARMM36 files from our site:

Re: [gmx-users] mdrun_command_not working in cygwin

Hi Wahab I do have Gromacs-4.6.3 installed on my cygwin but there also I am able to run all commands of gromacs except mdrun. sending the out put and mdlog of mdrun for 4.6.3. I do need Gromacs 4.5.4 as I have some comments in my paper where all work is done on this version. Please help.

[gmx-users] Atom-barycenter distance

Hi guys! Consider the atoms 1, 2 and 3 forming a triangle: I was wondering how can I calculate the barycenter of this triangle using the atoms coordinates? I want to measure the distance through time but I am not sure if there is a simple way to do it. Cheers! -- Marcelo Biochemicist

Re: [gmx-users] restraint the CM of a molecules in any one of the directions.

Dear Users, I am just resending the email. Constraining the CM of a molecules is a basic need of MD. Is that feature not available in Gromacs ? Thank you. On Wed, Nov 19, 2014 at 11:20 AM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi All, Is there a way to restraint the CM of a

Re: [gmx-users] restraint the CM of a molecules in any one of the directions.

On 11/24/14 7:13 PM, Sridhar Kumar Kannam wrote: Dear Users, I am just resending the email. Constraining the CM of a molecules is a basic need of MD. Is that feature not available in Gromacs ? You can accomplish something like this with the pull code, using no reference group, so each

[gmx-users] Regarding umbrella samplling

Hai gromacs users, Can we use the direction-periodic mdp option while running the samplling of windows instead of distance. The distance option was giving error that Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box size (15.033495) . So, for