Re: [gmx-users] Regarding calculation of angles

On 4/9/17 12:27 PM, Dilip H N wrote: Suppose for eg., in glycine how can i calculate the angle between nitrogen and hydrogen attached to it, angle between C alpha and H alpha etc., You can't calculate the angle between two angles; you need at least three. Regardless, you can easily just wri

Re: [gmx-users] Heavy metals parameterisation

On 4/9/17 6:04 AM, Alex Mathew wrote: Dear Gromacs users, I would like to study heavy metals (cadmium, mercury, lead, Arsenic, platinum and Chromium) interaction with proteins using charm36 ff. Where and how I can get parameters for these heavy metals ions.? If it is not available where i sho

Re: [gmx-users] Parameterization for noval molecules.

On 4/8/17 10:23 AM, maria khan wrote: Dear Gromacs users. Can anybody who are good in parameterization, make parameters for the molecule of my interest..As i am a beginner and was told on this forum that parameterization is not for beginners. You should identify someone (or several peopl

Re: [gmx-users] How to put excipients into the simulation box?

Hi, Using gmx insert-molecules before you solvate is a useful friend here. Mark On Sun, 9 Apr 2017 17:58 ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs Researchers, > Can I ask how to put excipients (e.g. sucrose, trehalose) into the > simulation box together with protein, salt and water?

[gmx-users] How to put excipients into the simulation box?

Dear Gromacs Researchers, Can I ask how to put excipients (e.g. sucrose, trehalose) into the simulation box together with protein, salt and water? Those excipients do not strongly interact with proteins, so they could not be treated as protein-ligand complex. I learned how to prepare the prote

Re: [gmx-users] Regarding calculation of angles

Suppose for eg., in glycine how can i calculate the angle between nitrogen and hydrogen attached to it, angle between C alpha and H alpha etc., Sent with Mailtrack

[gmx-users] Regarding calculation of angles

Hello, I have ran a amino acid simulation, and i want to calculate the angle between the atoms in amino acid molecule. how can i calculate it..?? gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]].. 1] here what index does it refer to .?? is it similar to the the RDF indexing ..??

Re: [gmx-users] LINCS

Thanks Joao. My problem was solved after I changed mdrun options. - Original Message - From: "João Henriques" To: gmx-us...@gromacs.org Sent: Sunday, April 9, 2017 4:44:22 PM Subject: Re: [gmx-users] LINCS Dear Neda, I'm not sure I appreciate the ellipses after "thanks". After all, I

Re: [gmx-users] LINCS

Dear Neda, I'm not sure I appreciate the ellipses after "thanks". After all, I took some of my personal time - on a Sunday - to do your work and Google search for the key words in your error message. Plus, I sent you the link and pointed you to the right section, which contains a crystal clear exp

Re: [gmx-users] LINCS

Thanks - Original Message - From: "João Henriques" To: gmx-us...@gromacs.org Sent: Sunday, April 9, 2017 3:37:46 PM Subject: Re: [gmx-users] LINCS Google is your friend, *always*. Please see the last section on: http://www.gromacs.org/Documentation/Errors /J On Sun, Apr 9, 2017 a

Re: [gmx-users] LINCS

Google is your friend, *always*. Please see the last section on: http://www.gromacs.org/Documentation/Errors /J On Sun, Apr 9, 2017 at 10:00 AM, Neda Rafiee wrote: > Dear gmx-users, > I have a problem in doing nv pequilibration for my pritein-water system, I > do not understand the error: > T

[gmx-users] Heavy metals parameterisation

Dear Gromacs users, I would like to study heavy metals (cadmium, mercury, lead, Arsenic, platinum and Chromium) interaction with proteins using charm36 ff. Where and how I can get parameters for these heavy metals ions.? If it is not available where i should start, to develop the parameters for t

[gmx-users] LINCS

Dear gmx-users, I have a problem in doing nv pequilibration for my pritein-water system, I do not understand the error: There is no domain decomposition for 16 ranks that is compatible with the given box and a minimu$ Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings