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,
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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
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
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-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
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
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Hi Periole, May be this website is useful for implicit solvent calculations.http://apbs.sourceforge.net/mohanOn 17/04/06,
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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
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
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