[gmx-users] TraPPE-EH in GROMACS

. Thanks and regards Dhrubajyoti Maji -- 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 * For (un)subscribe requests visit https

Re: [gmx-users] cut-off scheme

icular attention to the properties of your > interest, and on the properties on which the parameterization is based on > (if possible). The results should be very similar. > Best regards > Alessandra > > > > > On Tue, Jan 14, 2020 at 8:29 PM Dhrubajyoti Maji > wrote:

[gmx-users] cut-off scheme

use Verlet as it is default now? Any kind of help will be appreciated. Thanks and regards, Dhrubajyoti Maji -- 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

Re: [gmx-users] nrexcl value for ions

Thank you Prof. Lemkul for your kind reply. Dhrubajyoti On Sat, 4 Jan 2020 at 01:01, Justin Lemkul wrote: > > > On 1/3/20 12:10 AM, Dhrubajyoti Maji wrote: > > Dear gromacs users, > > A very happy new year to all of you. I an trying to simulate LiBr

[gmx-users] nrexcl value for ions

Chloride + urea, they have used nrecxl=3 for chloride ion. Here, I am confused about this. Any kind of help will be highly appreciated. Thanks and regards, Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] energy minimization

ential energy (not negative) guarantee the completion of EM process ? If so then what emtol value should I use ? Any help will be highly appreciated. Thanks for your time. Best regards Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/S

Re: [gmx-users] domain decomposition

Thank you sir. The problem is sorted out. Decreasing number of processors did the trick. Thanks again On Wed, 21 Aug 2019 at 22:02, Justin Lemkul wrote: > > > On 8/21/19 12:30 PM, Dhrubajyoti Maji wrote: > > Many tanks Dr. Lemkul for your kind reply. I have checked the link. I

Re: [gmx-users] domain decomposition

should have been failed. I am a newbie and I can't understand what exactly is going wrong. Any kind of suggestion will be highly appreciated. Thanks and regards. Dhrubajyoti Maji On Wed, 21 Aug 2019 at 16:21, Justin Lemkul wrote: > > > On 8/21/19 1:00 AM, Dhrubajyoti Maji wrote: >

[gmx-users] domain decomposition

with the issue. Thanks and regards. Dhrubajyoti Maji -- 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 * For (un)subscribe requests visit https

Re: [gmx-users] continue run

Thanks both of you for your useful suggestions. I'll check accordingly. Thanks again for help. Dhrubajyoti On Fri, 16 Aug 2019 at 15:50, Justin Lemkul wrote: > > > On 8/16/19 6:09 AM, Dhrubajyoti Maji wrote: > > Hi all, > > I have a simulated trajectory of 50 ns bu

[gmx-users] continue run

a 100 ns trajectory then what should I do? Any kind of help will be highly appreciated. Thanks and regards. Dhrubajyoti Maji -- 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

[gmx-users] gmx rdf

properties like density,dipole moment, dielectric constant, diffusion coefficient matches very well. Any suggestion will be highly appreciated. Thanks and regards. Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] topol. top file

, Jul 26, 2019, 12:43 Dhrubajyoti Maji wrote: > > > Dear gromacs users, > > I am writing the top file for liquid acetamide system > for > > OPLS FF. I am confused with the [pairs] section. Should I give the 1-4 > > atom numbers here or left it empty

[gmx-users] topol. top file

be written first , sigma or epsilon ? Thanks and regards Dhrubajyoti Maji -- 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 * For (un)subscribe

Re: [gmx-users] There is no domain decomposition error

Hi, Thanks Mr. Bauer for your help. Actually, I was running grompp in desktop and the mdrun in cray. Now I am running both in cray and it runs fine. Thanks again. Dhrubajyoti Maji On Mon, 10 Jun 2019 at 20:38, Paul bauer wrote: > Hello, > > did you change the command

[gmx-users] There is no domain decomposition error

same except for number of steps. Could you please tell what is going wrong and how to solve it ? Thanks in advance. Dhrubajyoti Maji -- 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

Re: [gmx-users] ENERGY MINIMISATION

sing -pbc mol by gmx trjconv command. Hope this > will work otherwise it is your system error, you need to modify your > molecule topology file. > - Message from Dhrubajyoti Maji - > Date: Thu, 6 Jun 2019 11:23:36 +0530 > From: Dhrubajyoti Maji > Reply-To: gmx-

[gmx-users] ENERGY MINIMISATION

this problem. Thanks Dhrubajyoti Maji -- 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 * For (un)subscribe requests visit https

[gmx-users] LINCS error during EM

Dear all, The gmx dielectric command gives negative value of imaginary part in gromacs-2018.3. I can't get the reason. It will be highly helpful if someone make a suggestion. Thank you. Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] gmx trjconv

and gro file ? If there is data loss is it significant enough to produce erroneous result? Thanks and regards, Dhrubajyoti Maji -- 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

Re: [gmx-users] inconsistency in xvg file

ll investigate fixing it. > > > > Mark > > > > On Tue, 30 Apr 2019 at 08:11, Dhrubajyoti Maji > wrote: > > > >> Dear GROMACS users, > >> I am using gromacs-2018.3. My system is molten > >> acetamide. Run time is 50 ns and sa

[gmx-users] Query about gmx dipoles

Hi all, I am using gromacs - 2018.3. I want to use the gmx dipoles command for a mixture of two components. Do I have to run this command twice for two groups with their respective mu values? I find difficulty in assigning the mu_max value. How to calculate the value ? Any suggestions

[gmx-users] gmx dipoles

Hi all, In gromacs version 2018.3 , using gmx dipoles require the value of mu and mu_max . How to give the values for a mixture of more than one component? What is the relation between mu and mu_max? Any suggestions are welcome. Thanks in advance.