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

ion list for GROMACS users <gmx-users@gromacs.org>Message-ID: <[EMAIL PROTECTED]>Content-Type: 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 va

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

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 unsub

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

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 thi

[gmx-users] Re: Molecular volume

4. Re: Atom q2 not found in rtp database in residue TRP (Joern Lenz)   5. Re: Fw: 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:

[gmx-users] Molecular volume

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: 1-713-743-

[gmx-users] Error installing gromacs on solaris system

Dear all, I got the following error message while trying to install gromacs on a cluster running on solaris operating system. FFTW installed successfully. Could anyone help ?Undefined   first referenced  symbol in file__floatdidf  

[gmx-users] using ffgmx force field

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-u

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

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

c. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,  75124 Uppsala, Swedenphone:  46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED]    http://folding.bmc.uu.se++

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

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