Re: [gmx-users] Ion Polarizability (Shell Model)

Eric Shamay wrote: In researching the shell model used to create "polarizable" ions I came across several of the references of the drude oscillator approach and the papers of van der Spoel (for the SW water model) and Roux (for the parameters of the halides and alkalis). However, perhaps due to

[gmx-users] about g_wham

Hi all, Could you please tell me why g_wham does not give the correct result? After doing umbrella sampling with mdrun, I got the .pdo file which is like # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'DPP' # Nr. of pull groups 1 # Group 1 'PIP' Umb. Pos. 3.3885

[gmx-users] Ion Polarizability (Shell Model)

In researching the shell model used to create "polarizable" ions I came across several of the references of the drude oscillator approach and the papers of van der Spoel (for the SW water model) and Roux (for the parameters of the halides and alkalis). However, perhaps due to my own oversight, I di

Re: [gmx-users] Urea topology problem

Rebeca García Fandiño wrote: Hello, I don´t understand the correction I should do from itp. I have removed from the urea original urea.itp these lines, don't use this model. do a proper literature search. #ifdef Boek 1 C 1UREA C1 1 0.38 2 O

Re: [gmx-users] Urea topology problem

Rebeca García Fandiño wrote: Hello, I don´t understand the correction I should do from itp. I have removed from the urea original urea.itp these lines, The error message was that grompp couldn't find masses for these atoms. The correct format should include a mass column after the charge

RE: [gmx-users] Urea topology problem

Hello, I don´t understand the correction I should do from itp. I have removed from the urea original urea.itp these lines, #ifdef Boek 1 C 1UREA C1 1 0.38 2 O 1UREA O2 1 -0.38 3 NT 1UREA N3 2 -0.83

[gmx-users] chcl3.itp Invalid order for directive atom types

Hi Mohana, please be more specific (what mail did you read? what exactly is your problem, .itp, .top, command, etc.) and please post to the mailing list. If you would like to draw my attention to your post, then you can send me a separate email notifying me that you have posted something

Re: [gmx-users] Gromacs 4 with mpi interface

On Thu, 2008-12-18 at 21:23 +0530, Manik Mayur wrote: > I am not sure that mdrun_mpi or for that matter mdrun with options -np > 2 -multi 1 (I have a core 2 duo machine) is actually running the > process parallely, as the estimated time for completion for a > simulation is the same as without. You

Re: [gmx-users] Gromacs 4 with mpi interface

I am not sure that mdrun_mpi or for that matter mdrun with options -np 2 -multi 1 (I have a core 2 duo machine) is actually running the process parallely, as the estimated time for completion for a simulation is the same as without. I have built open-mpi library, so do I have to make some changes

Re: [gmx-users] Urea topology problem

Rebeca García Fandiño wrote: ERROR 1 [file solvated.top, line 39]: atom C1 (Res UREA-1) has mass 0 In urea.itp, no masses are defined. If you correct the format of this file (see Chapter 5 of the manual), then this issue should be resolved. Which force field does this urea.it

[gmx-users] Urea topology problem

Hello, I would like to simulate a proteína in urea, using Gromacs. I have tried to use the box included in Gromacs by default (urea+h2o.gro and urea.itp). The topology of the urea/water-solvated protein is: ; Include forcefield parameters #include "ffG43a2.itp" #include "protein.itp" ; In

[gmx-users] TI with nonbond_params

Hi, I'm running a TI perturbing the lennard jones parametters of an ion. In addition I have specified the lj interaction of that ion with water using nonbond_params like this: #include "ffG53a6.itp" [ atomtypes ] ;name at.num mass charge ptypec6 c12 NaMod CA1 0.

Re: [gmx-users] Dear Sir !

On Dec 18, 2008, at 10:25 AM, Venkat Reddy wrote: how to save the coordinates of atoms at regular intervals that were generated during "mdrun" ?? Is it automatic or we need to modify .mdp file Hi, The 'nstxout' and 'nstxtcout' entries in the mdp file allow you to set how often the c

RE: [gmx-users] Re[2]: What water topology is worth using?

Ah, I can advertise my own work again. We have shown that SPC/E is probably the best water model for use with most biomolecular force fields, although TIP4p is not much worse, SPC and TIP3P perform worse, especially at temperatures far from 300 K. http://dx.doi.org/10.1021/jp0641029 Berk > Date:

Re: [gmx-users] About the -multi option in mdrun

Lee Soin wrote: Hello! How to specify the -multi option when doing REMD with mdrun? It seems that this option has changed from bool to int type in version 4.0. mpirun -np 24 mdrun -multi 4 will start 4 jobs at 6 processors each. -- Sun Li Department of Physics Nanjing University, China --

[gmx-users] About the -multi option in mdrun

Hello! How to specify the -multi option when doing REMD with mdrun? It seems that this option has changed from bool to int type in version 4.0. -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Dear Sir !

how to save the coordinates of atoms at regular intervals that were generated during "mdrun" ?? Is it automatic or we need to modify .mdp file Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-u