[gmx-users] user defined potential function for 1-4 interaction

Hi All: I have two separate problems for this subject. 1) What should be the way to pass a formatted table for the 1-4 interaction for two different groups? Reading page 150 and 180 of manual 4.0, I understand user defined potential functions can be passed for many groups using energygrp_tab

Re: [gmx-users] user defined potential function for 1-4 interaction

Hi all: I posted this earlier but did not get any help I really need to slove this issue. What should be the way to pass a formatted table for the 1-4 interaction for two or more different groups? Reading page 150 and 180 of manual 4.0, I understand user defined potential functions can be

Re: [gmx-users] user defined potential function for 1-4 interaction

I think there must be a way in gromacs to pass tabulated potenttial for 1-4 interaction for two groups as interaction between different pairs can be significantly different and can change the structure of an indiviual molecule. I would request: Please let me know if it is possible to pass tabul

[gmx-users] SD simulation of Ethane and Methane

Hi all: I tried to produce the distribution of ethane using SD integrator of GROMACS 4.0. It appears that the distribution obtained from SD is different from the one obtained using MD. However, I can produce the distribution of Methane using SD that matches the one obtained using MD. Distibut

Re: [gmx-users] user defined potential function for 1-4 interaction

Hi Berk: Thanks for your eply. I guess I would supply two column in the table for the bond type 9 [r(nm) and W(kJ/mol) ]. In that case (according to the user manual) what is the significance of k? how k will come into the calculation? If I select "constraints = all bond" will that affect bond

[gmx-users] Langevin Dyanamics in GROMACS

Hi all: Anyone can help me using Langevin Dynamics in GROMACS. Where does the friction coefficient goes and How we can change the forece field to include PMF. Thanks, M. Rahman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/m

Re: [gmx-users] Langevin Dyanamics in GROMACS

tin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Friday, February 13, 2009 5:51 PM Subject: Re: [gmx-users] Langevin Dyanamics in GROMACS M Hafizur Rahman wrote: Hi all: Anyone can help me using Langevin Dynamics in GROMACS. Where does the friction coefficient