Re: [gmx-users] GAAMP parameterization

2017-05-01 Thread David van der Spoel
On 02/05/17 06:06, Mohsen Ramezanpour wrote: Hi Everyone, I would like to know your opinion on these questions. I highly appreciate your comments in advance. You could at least at the address of the server and tell in one line what it is supposed to do. You should never mix force fields

Re: [gmx-users] Calculation of volume of protein hydration layer

2017-05-01 Thread David van der Spoel
On 01/05/17 18:44, Saumyak Mukherjee wrote: Dear Users, Can anybody please tell me how to calculate the volume of protein hydration layer as a function of time? Apart from this I would also like to calculate the volume of second hydration shell around a protein. I can define hydration layer in

Re: [gmx-users] GAAMP parameterization

2017-05-01 Thread Mohsen Ramezanpour
Hi Everyone, I would like to know your opinion on these questions. I highly appreciate your comments in advance. Cheers, Mohsen On Thu, Apr 27, 2017 at 10:23 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > Using GAAMP server for parameterization, if the

Re: [gmx-users] Polymer topology file

2017-05-01 Thread Justin Lemkul
On 5/1/17 1:05 PM, Chetan Puri wrote: Is there any example or tutorial for building a polymer topology/itp file. First Google result for "GROMACS polymer" is http://www.gromacs.org/Documentation/How-tos/Polymers :) -Justin -- == Justin A.

Re: [gmx-users] gmx hbond -tu error

2017-05-01 Thread Justin Lemkul
On 5/1/17 10:15 AM, Marcelo Depólo wrote: Hi! I am running ACF calculations in gmx hbond tool in 5.0.7 version. When running: gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg and gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg The results given for

[gmx-users] gmx sorient interpretation

2017-05-01 Thread Marcelo Depólo
Hi, I am not sure how to interpret the cos(theta1) around my reference atom. The help printed is not straightforward when comes to set which atoms forms the angle theta1. For instance. "theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms

[gmx-users] Polymer topology file

2017-05-01 Thread Chetan Puri
Is there any example or tutorial for building a polymer topology/itp file. I need for PVP. -- 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

[gmx-users] Calculation of volume of protein hydration layer

2017-05-01 Thread Saumyak Mukherjee
Dear Users, Can anybody please tell me how to calculate the volume of protein hydration layer as a function of time? Apart from this I would also like to calculate the volume of second hydration shell around a protein. I can define hydration layer in two ways: 1. g_select 2. trjorder If this

[gmx-users] gmx hbond -tu error

2017-05-01 Thread Marcelo Depólo
Hi! I am running ACF calculations in gmx hbond tool in 5.0.7 version. When running: gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg and gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg The results given for the ACF are completely different (example:

Re: [gmx-users] 2016.3 installation

2017-05-01 Thread RAHUL SURESH
Dear Mark First apology that I am unaware how to run the test programs. Next, I tried to simulate a protein and i get the following error. *[user@mqml rahul]$* source /usr/local/gromacs/bin/GMXRC *[user@mqml rahul]$* gmx pdb2gmx -f 99nsInput.pdb -o 99nsInput.gro -p 99nsInput.top gmx: