Re: [gmx-users] Since nstlist has no effect on the accuracy

...@gromacs.org. -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail: iglad...@sissa.it web page: http://people.sissa.it/~igladich/ -- Gromacs Users mailing list * Please

[gmx-users] About pdb2gmx and cyclic peptides

is that I have thousand of structures and so I need to do it iteratively. I am wondering if in the newer versions of gromacs the problem has been addressed and solved. Thanks for any possible advice Ivan -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies

Re: [gmx-users] Regarding the Pi-Pi and pi-cation interaction

Hi, to the best of my knowledge, Molecular Dynamics is not the best way to study system stabilized by Pi-Pi or Pi-Cataion interaction. However,in MD people usually overpolarized C-C and C-H bonds to increase the quadrupole interactions, and thus, mimic the Pi-Pi interaction See

Re: [gmx-users] Regarding the Pi-Pi and pi-cation interaction

On 2014-10-30 13:10, Justin Lemkul wrote: On 10/30/14 4:57 AM, Ivan Gladich wrote: Hi, to the best of my knowledge, Molecular Dynamics is not the best way to study system stabilized by Pi-Pi or Pi-Cataion interaction. However,in MD people usually overpolarized C-C and C-H bonds to increase

Re: [gmx-users] Simulations with Verlet scheme, virtual sites and heterogeneous systems

Dear Mark thanks for your reply. As you suggested, I will try with the version 5.0.4 and I will test the setup this water model with Verlet and in bulk water. I will keep you posted Ivan On 04/27/2015 03:04 PM, Mark Abraham wrote: On Mon, Apr 27, 2015 at 12:26 PM, Ivan Gladich iglad

[gmx-users] Simulations with Verlet scheme, virtual sites and heterogeneous systems

to the energy drift is approximated. In most cases this does not affect the energy drift significantly. 3) Is there a way to go around this issue? With GPU+Verlet and I doing ~110 ns/day while, with group+CPU 33 ns/day Thanks for any possible help or suggestions Sincerely Ivan -- -- Ivan

Re: [gmx-users] Query about a simple MD with constant electric field

for your help Ivan On 2016-03-09 20:10, David van der Spoel wrote: On 09/03/16 11:48, Ivan Gladich wrote: Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion

Re: [gmx-users] Query about a simple MD with constant electric field

? They can certainly mess up an accelerating system. Kind regards, Erik On 10 Mar 2016, at 10:33, Ivan Gladich <iglad...@sissa.it> wrote: Dear Prof. Spoel first of all thank you for your reply. 1) No, I did not get any warning about PME and charge system, just a note NOTE 4 [file top

[gmx-users] Query about a simple MD with constant electric field

Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion is not coupled to the thermostat and it is placed in a box of 4 nm* 4nm * 16 nm, in the X,Y,and Z

[gmx-users] 100-quartz force field for GROMACS using CGenFF

Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental material of Lopes, P.E.M., Murashov,

Re: [gmx-users] 100-quartz force field for GROMACS using CGenFF

Dear Justin, thank you for your prompt answer. I will contact you off-list. Best Ivan On 2017-03-05 17:14, Justin Lemkul wrote: On 3/5/17 6:56 AM, Ivan Gladich wrote: Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force