Re: [gmx-users] About using GLYCAM force field in Gromacs

you can try charmm-gui Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn * On Tue, May 23, 2017 at 11:20 AM, 维维 wrote: > Dear

Re: [gmx-users] Fraction of native contacts.

Hi, Prakash： you can try mdtraj. http://mdtraj.org/1.8.0/examples/native-contact.html Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn * On

Re: [gmx-users] Distance restraint between two chains' com

Lemkul jalem...@vt.edu wrote: On 2/6/15 8:47 AM, WT Ren wrote: Dear Justin: Sorry to bother you again When I did a long flat-bottom distance restraint(about 2nm), I got the error message: “There is no domain decomposition for 8 nodes” So is there any way to do a long distance restraint

Re: [gmx-users] Distance restraint between two chains' com

of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn* On Thu, Feb 5, 2015 at 7:51 PM, WT Ren rener...@gmail.com wrote: Dear Justin: Many thanks for your reply. I would like to test

Re: [gmx-users] Distance restraint between two chains' com

Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn* On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/5/15 2:39 AM, WT Ren wrote: Dear Gromacs Users, I am trying to apply

[gmx-users] Distance restraint between two chains' com

Dear Gromacs Users, I am trying to apply a distance restraint between two chains' center of mass to prevent them diffusing far away from each other. As I known, the pull code seems only can restrain the distance to a reference distance with harmonic potential, while the distance restraint seems

[gmx-users] Distance restraint between two chains' com

Dear Gromacs Users, I am trying to apply a distance restraint between two chains' center of mass to prevent them diffusing far away from each other. As I known, the pull code seems only can restrain the distance to a reference distance with harmonic potential, while the distance restraint seems

[gmx-users] Reference group in COM pulling

Dear all: Recently, I'm using COM pulling to unfold a protein. So I'm wondering how the gromacs deal with the reference group. Is the reference group fixed, constrained or free? Many thanks in advance. Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing