[gmx-users] Re: query TFE gro and itp file

2006-11-13 Thread Mohan Boggara
Dear Chiradip, May be try using PRODRG. Type PRODRG in google, and then draw your molecule, it will generate a topology and gro file for you. Mohan On 12/11/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions togmx-users@gromacs.orgTo subscribe or unsubscribe

[gmx-users] Re: Re: How to generate GRO and TOP file for

2006-11-13 Thread Mohan Boggara
: text/plain; charset=ISO-8859-1; format=flowed Mohan Boggara wrote: However, to extend the gro file, we need to use the angle information and may be write a script.Molecule builders in various chemistry packages may be of help here. You may need to use a text editor to change atom and residue names

[gmx-users] Re: How to generate GRO and TOP file for

2006-11-11 Thread Mohan Boggara
Dear Wu, I had exactly the same question to ask the users. I hope someone would give a better idea to generate gro and itp for a polymer of your choice molecular weight. Currently, what I am doing is to create a smaller polymer using prodrg and manually extend the itp to the size I want. I know

[gmx-users] Molecular volume

2006-11-06 Thread Mohan Boggara
Dear users, Is there a way to calculate molecular volume of small solutes that we use in simulations?Mohan -- Mohan BoggaraGraduate Research AssistantDept of Chemical Engineering University of HoustonS222 Engg Bldg 1, 4800 Calhoun Rd,Houston, Texas-77204, USAMobile: 1-832-643-5729Office:

[gmx-users] Re: Molecular volume

2006-11-06 Thread Mohan Boggara
: gmx-3.3.1_cpmd-3.11.1 with mpirun (Pradip K Biswas) 6. Re: (dH/dl) calculation (David Mobley) 7. Molecular volume (Mohan Boggara) 8. Re: Molecular volume (David Mobley)--Message: 1Date: Mon, 6 Nov 2006 12:03:33 +0100From: Joern Lenz

[gmx-users] using ffgmx force field

2006-04-27 Thread Mohan Boggara
Hi, In the file FF.dat, it is mentioned that GROMACS force fields ffgmx and ffgmx2 are DEPRECATED in the brackets. Does it mean I should not use it?Can someone help me with this?Mohan On 27/04/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to

[gmx-users] Re: questions about implicit solvent simulation

2006-04-17 Thread Mohan Boggara
Hi Periole, May be this website is useful for implicit solvent calculations.http://apbs.sourceforge.net/mohanOn 17/04/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions togmx-users@gromacs.orgTo subscribe or unsubscribe via the World Wide Web, visit

[gmx-users] Re: Using Pull code with Coarse grain model

2006-04-13 Thread Mohan Boggara
o 20 or 50. Mohan -- Mohan Boggara Department of Chemical Engineering University of Houston S222 Engineering Bldg 1 Houston, Texas-77204, USA Mobile: 1-713-259-2166 Office: 1-713-743-4314 http://polymer.chee.uh.edu/ All human actions have one or more of these seven causes: chance, nature, compuls

[gmx-users] Using Pull code with Coarse grain model

2006-04-12 Thread Mohan Boggara
Hi all, I am trying to use the pull code for constrained force method in a coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am getting error message Warning: pressure scaling 1% . The problem persist even after I changed the tau_p from 1.0 to 1.5. Has anyone had any success on