[gmx-users] Feature wishlist

to constraint the CM of a molecules in the Z direction. constraint-group = molecule constraint-k = 500 constraint-dim = N N Y Thanks. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

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

is at the mid point of simulation box. The option pull_geometry=position is removed from the 4.5 version, right ? or is it only missing from the manual ? Best, On Thu, Jan 8, 2015 at 3:52 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/6/15 9:48 PM, Sridhar Kumar Kannam wrote: Hi Justin

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

9:31 AM, Sridhar Kumar Kannam wrote: Hi Justin, Please see Figure 1 of the attached paper. I have a SiN nanopore/membrane with the solvent on both the sides. The protein is inside the pore as in Figure 1a. Let say the pore axis is along the z-axis. I want to constraint the CM

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

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

freely, applying the atomic position restraints do the job but it prevent the rotation of the molecule. Any suggestions ? Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] strange behaviour of gmx solvent with non standard solvent

/2014/protein-tutorial/hiv-1_protease.tgz) - http://md.chem.rug.nl/cgmartini/index.php/proteins Any ideas ...? Than you. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Martini force field - coarse grained protein tutorials

you tried clicking on the .mdp file names in the commands, which are underlined and highlighted in blue? Seems to work for me. Cheers, Tsjerk On Sep 14, 2014 12:41 PM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi All, I am a newbie to Gromacs and Martini force field. I begin

[gmx-users] Martini force field - coarse grained protein tutorials

getting different kinds of error. As I have not read the manual yet, its hard to debug the errors. Can someone please share the *mdp files to run this tutorial (Ubiquitin and HIV-Prtease) simulations. Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please

[gmx-users] Martini force field for inhibitors

inhibitor ? Sorry for the naive question ... Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- 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 http://www.gromacs.org/Support/Mailing_Lists