[gmx-users] RE: Covalent bonds breaking formation

> What software instead of gromacs can I use to treat chemical reactions > properly. > (See Chapter 1 page 4 of manual-3.3.pdf) CPMD, VASP, Quantum-ESPRESSO. What about using google? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svobody sq.,4, Kharkiv 61077, Ukraine ema

Re: [gmx-users] ffamber and ions

hi Alan, Can you show us your modified ions.itp file (just the Cl part) and the exact command options you used for genion? Thanks, Vignesh On Thu, Jul 3, 2008 at 2:44 PM, Alan <[EMAIL PROTECTED]> wrote: > Hi List, > To people using ffamber. > > I have ffamber with ions.itp modified to recognise f

[gmx-users] about itp file making

Hi, This is first time that I am sending mail so I do not know the where I have to send for proper answer of my question. To make .itp file of a sugar molecule, what should be the gromacs force field (96/opls)? regards Anirban ___ gmx-users mailing l

[gmx-users] Re: minimisation and constraints

Thanks Peyman and Justin, So, bottom line, if doing any sort of minimisation (even cg), 'constraints = none' is fine, right? Alan On Wed, Jul 2, 2008 at 7:44 PM, Alan <[EMAIL PROTECTED]> wrote: > Dears, > It's more than years that I don't use GMX on regular basis so my memory is > leaking here.

[gmx-users] Dynamics : ONE dihedral angle time resolution

Hi I want to get the dynamics of ONE dihedral angle time resolution. g_angle computes the angle distribution for a number of angles or dihedrals. With option -ov I can plot the average angle of a group of angles as a function of time. I don't want the average angle of a group of dihedral angle as

[gmx-users] the .mdp format

Hi I did not fully understand about this command. Could anyone explain this more? Thanks a lot include: directories to include in your topology. Format: -I/home/john/my_lib -I../more_lib Lin ___ gmx-users mailing listgmx-users@gromacs.org http://ww

Re: [gmx-users] Dynamics : ONE dihedral angle time resolution

On Thu, 3 Jul 2008 01:01:53 -0700 "Chih-Ying Lin" <[EMAIL PROTECTED]> wrote: Hi I want to get the dynamics of ONE dihedral angle time resolution. g_angle computes the angle distribution for a number of angles or dihedrals. With option -ov I can plot the average angle of a group of angles as a f

[gmx-users] How to analyze order parameter

Hi, I want to find deuterium order parameter of the system of DPPC+SM+CHOL+WATER g_order -f traj.trr -s topol.tpr -n index.ndx -dt 0.001 it gives the following error: Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 3.3.3 (single precision) Using following

[gmx-users] Re: ffamber and ions

So, as requested: for ions.spc I got info from http://www.somewhereville.com/?p=114 In attach files you may need to reproduce what I am doing here. Assuming you have ffamber installed and GMX 3.3. Copy ions.itp and tip3p.itp to your _gromacs_/top/ folder. tip3p.itp was modified by me. I use Mac

[gmx-users] ffamber and ions

Sorry, sending again in plain txt So, as requested: for ions.spc I got info from http://www.somewhereville.com/?p=114 In attach files you may need to reproduce what I am doing here. Assuming you have ffamber installed and GMX 3.3. Copy ions.itp and tip3p.itp to your _gromacs_/top/ fold

RE: [gmx-users] How to analyze order parameter

First, make an index file that contains one group each for every carbon atom in the acyl-chain (starting with the carbonyl-carbon and going further down). You need to make two index files: for sn1 and sn2 chains of DPPC Then you get the deuterium order parameters for each atom with the output o

[gmx-users] RE: the .mdp format

> I did not fully understand about this command. > Could anyone explain this more? > Thanks a lot > > include: > directories to include in your topology. Format: > -I/home/john/my_lib -I../more_lib This is a directory where your topology files are placed, isn't it? -- Vitaly V. Chaban School of

Re: [gmx-users] about itp file making

Use whichever one you think will best represent your molecule. I think some work was done with sugars in G96 45a3, if I'm not mistaken. -Justin anirban polley wrote: Hi, This is first time that I am sending mail so I do not know the where I have to send for proper answer of my question.

Re: [gmx-users] RE: the .mdp format

Vitaly Chaban wrote: I did not fully understand about this command. Could anyone explain this more? Thanks a lot include: directories to include in your topology. Format: -I/home/john/my_lib -I../more_lib This is a directory where your topology files are placed, isn't it? More or

Re: [gmx-users] about itp file making

Hi Anirban, Might it be of any use, here's a structure/topology of glucose based on the GROMOS96 53a6 force field. Hope it helps, Tsjerk On Thu, Jul 3, 2008 at 12:44 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Use whichever one you think will best represent your molecule. I think some >

Re: [gmx-users] about itp file making

Darn.., forgot the attachment. > > On Thu, Jul 3, 2008 at 1:16 PM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: >> Hi Anirban, >> >> Might it be of any use, here's a structure/topology of glucose based >> on the GROMOS96 53a6 force field. >> >> Hope it helps, >> >> Tsjerk >> >> On Thu, Jul 3, 2008

[gmx-users] Re: Dynamics : ONE dihedral angle time resolution

Or add option -all if you have several... servaas Message: 2 Date: Thu, 03 Jul 2008 10:36:56 +0200 From: "Xavier Periole" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Dynamics : ONE dihedral angle time resolution To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-T

[gmx-users] RE: about itp file making

> Hi, > This is first time that I am sending mail so I do not know the where I > have to send for proper answer of my question. To make .itp file of a sugar > molecule, what should be the gromacs force field (96/opls)? > regards > Anirban It's not critical what force field to use for making t

[gmx-users] QMMM memory problem

Hello all: I'm tryng to perform a QM/MM simulation and the following error arises inmediatly: " number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault " I understand that this is an insufficien

[gmx-users] .mdp format

Hi if I am in my working directory, and give the command in my .mdp file include =-I/my_working_directory I will get the following error Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (xxx.gro, 24)

[gmx-users] Re: .mdp format

Chih-Ying Lin wrote: Hi if I am in my working directory, and give the command in my .mdp file include =-I/my_working_directory I will get the following error Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 469 Fatal error: number of coordinates in coordinate file

[gmx-users] Re: .mdp format

Hi I think that include =-I/my_working_directory is redundant and that is the fatal error coming from.. without this command (delete from my .mdp file) include =-I/my_working_directory my simulation get run Thanks Lin On 7/3/08, Justin A. Lemkul <[EMAIL PROTECTED]>

[gmx-users] Force Field: A new chemical compound

Hi Honestly, I don't know how to do the quantum chemistry calculation. I have the one azobenzene derivative force field parameters(from QM/MM paper) in hand. This azobenzene derivative is quite similar with the azotab compound, which I need. For the rest parts of the azotab compound I try to used

Re: [gmx-users] mass changes in free energy calculations

Yes, usually it would be a waste of time and energy to change the mass. On Fri, Jun 20, 2008 at 10:17 PM, Qiang Li <[EMAIL PROTECTED]> wrote: > Thanks for clearing the doubt. > > Is that more easier to get equlibrium to use unchanged mass when doing LJ > turning on/off? > I ask this since I found

Re: [gmx-users] Force Field: A new chemical compound

Chih-Ying Lin wrote: Hi Honestly, I don't know how to do the quantum chemistry calculation. I have the one azobenzene derivative force field parameters(from QM/MM paper) in hand. This azobenzene derivative is quite similar with the azotab compound, which I need. For the rest parts of the azota

[gmx-users] Re: QMMM memory problem

Could you privide more specific info about what system you ran, which gromacs version, and how gromacs was configured? Gerrit Hello all: I'm tryng to perform a QM/MM simulation and the following error arises inmediatly: " number of CPUs for gaussian = 1 memory for gaussian = 5000 a

Re: [gmx-users] Re: QMMM memory problem

Yes. The system is a methane molecule with 30 waters (from spc). There are about 95 atoms. The QM subsystem is the methane. The GROMACS version is 3.3.1 and it was instaled (in single precision) in an AMD Athlon64 with Fedora Core 5 and 1.5 Gb RAM. The options in .mpd file are: QMMM        = ye

[gmx-users] segmentation fault during MD

Dear gmx users n developers. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe reques

[gmx-users] segmentation fault during MD

Dear gmx users and developers. I was running a simulation with 5 ns. But it stated "segmentation fault" at time around 1 ns, and the simulation was stopped. By the way, i faced 2 warning during running the Grompp, it stated there:" warning 1 No default Ryckaert-Bell types, using zeroes"