Re: [gmx-users] Re,i don't know how can i determine emtol

ahoney and Jorgensen, J. Chem. Phys., 2000, VOLUME 112, NUMBER 20 2) S. W. Rick, J. Chem. Phys., 2004, 120, 6085–6093. All the best Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Fleming

Re: [gmx-users] Re,i don't know how can i determine emtol

Sincerely Ali Alizadeh On 11/21/2012 09:43 AM, Ivan Gladich wrote: Dear Ali the paper that you are citing is using a rigid TIP4P water model As far as I know, emtol is relevant only for minimization or molecular dynamics with shell particle or flexible constraints. Therefore, as Justin

Re: [gmx-users] Re,i don't know how can i determine emtol

rigid TIP4P model of water? 2) I would rather use other water model that have been explicitly tested for Ice (e.g. TIP4P/2005, TIP4P/Ice, TIP5P-Ew, NE6) Best Ivan Sincerely Ali Alizadeh On 11/21/2012 09:43 AM, Ivan Gladich wrote: Dear Ali the paper that you are citing is using a rigid

Re: [gmx-users] Re,i don't know how can i determine emtol

ibe in full what you are doing, and provide answers to all the >questions posed above, or else I'm afraid I'm not going to have anything else >useful to say. -Justin -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of th

[gmx-users] Fast Question on g_msd

Dear all I am running a simulation of water slab, i.e. a water system with two air/vacuum interface, using a 5 site water model. I am doing a simple test calculating the water diffusivity by mean square displacement in different regions of my water slab. In order to do, I created an index that

Re: [gmx-users] Chemical Potential

chemical potential...but I do not want to say you something wrong since I do not have experience in such systems. Good luck Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo nám. 2

Re: [gmx-users] g_msd bug

...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo nám. 2. 166 10 Praha 6 Czech Republic Tel:

[gmx-users] g_msd uncertainty

efficient on the two halves of the fitting region (first method)? I was searching in the mail list without success...thanks for any help Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.

[gmx-users] g_select and make_ndx

xes that are common between all the groups.. make_ndx > "group1" & "group2" but now I have 1 groupsand I think I will have also problem with the name length Is there a smarter way to do that? thanks a lot for any comment or suggestions Best Regards Iv

Re: [gmx-users] g_order for water

inside the group? Thank you again Ivan On 05/05/2011 02:33 PM, Ivan Gladich wrote: Dear all I am simulating a water slab using a 6-site water model and I would like, for each time step, to calculate the tetrahedrality order parameter of every water oxygens using the four nearest neighbour

[gmx-users] g_order for water

backed up sliced.xvg to ./#sliced.xvg.3# gcq#260: "I Quit My Job Blowing Leaves" (Beck) ### By the way, if I look the file order.xvg, it is empty Did I miss something? I searched in the web for some hint without success... thank you for any help, I

[gmx-users] Re: polarizable water models

romacs.org <mailto:gmx-users-ow...@gromacs.org> When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: polarizable water models (Mark Abraham)

Re: [gmx-users] polarizable water models

hanks alot Regards Saly -- Message: 3 Date: Wed, 27 Apr 2011 12:14:42 +0200 From: Ivan Gladich mailto:ivan.glad...@marge.uochb.cas.cz>> Subject: Re: [gmx-users] POL3 water model To: Discussion list for GROMACS users mailto:gmx-use

Re: [gmx-users] POL3 water model

used LAMMPS but it has not polarizable water models. Therefore I want to use GROMACS. I need .itp and .mdp files of POL3 water model. Do you have the files. Would you please help me. Thanks alot for your time and attention Regards Saly -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow

Re: [gmx-users] Annealing of shell polarizable water model

temperature (K) tau_t= 0.1 ref_t= 160.00 ## On 03/22/2011 01:09 PM, Justin A. Lemkul wrote: Ivan Gladich wrote: Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still

Re: [gmx-users] Annealing of shell polarizable water model

without problem. So I do not think that it is a problem of the shell polarizability with the running in parallel. Could be a problem of the shell polarizability with annealing? Thanks again Ivan On 03/22/2011 10:45 AM, Ivan Gladich wrote: Yes, I am running in parallel... Now I will try to run

Re: [gmx-users] Annealing of shell polarizable water model

Yes, I am running in parallel... Now I will try to run in serial to see if the problem persist Thanks Ivan On 03/22/2011 10:00 AM, David van der Spoel wrote: On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of

[gmx-users] Annealing of shell polarizable water model

= yes gen_temp = 0 gen_seed = 1993 ;CONSTRAINTS constraints = hbonds constraint_algorithm = LINCS -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and

Re: [gmx-users] defining a 3 body user defined potential

this help Ivan Amit Choubey wrote: > Hi all, > > I was wondering if there is a way to define user defined potential which > involves 3 particles. Thank you for any input. > > > Amit > > -- --- Ivan Gladich, Ph.D. Dreyfus Postdoctoral Fellow Department of Chem

[gmx-users] distance restraints in Gromacs 4.0.4

any problem. Do you know what kind of problem could be? Has the version 4.0.4 some problems with distance restrains? Thank you in advance for any help or suggestion Ivan Gladich -- --- Ivan Gladich Dreyfus Postdoctoral Fellow Department of Chemistry Purdue University 560 Oval Drive