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

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. Flemingovo nám. 2

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

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 the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i

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

[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

the 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

-users-requ...@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

[gmx-users] g_msd uncertainty

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.i. Flemingovo nám. 2. 166 10

[gmx-users] g_select and make_ndx

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 Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy

[gmx-users] g_order for water

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, Ivan -- -- Ivan Gladich

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] Re: polarizable water models

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) 2. Re: polarizable water models (Ivan Gladich

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] polarizable water models

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

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

[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

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

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 Chemistry Purdue University 560 Oval

[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