[gmx-users] Some questions on Tabulated Dihedral Potential

Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning

回复： [gmx-users] Re: Some questions on T abulated Dihedral Potential

Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviat

回复： 回复： [gmx-users] Re: Some ques tions on Tabulated Dihedral Potential

es in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote:

[gmx-users] Two Types of van de Waals interactions in one system

Dear all, Has anyone tried to use 2 van de Waals interaction types in one system? For example, the system includes two components A and B. The van de Waas interaction for A is LJ type, while for B Buckingham form is used. Can GROMACS support two forms simultaneously? Thanks Cynthia ___

[gmx-users] Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?

Dear all, I'm trying to simulate multiple phases in one system. Each phase has distinct van der Waals potential form and different cutoffs from the rest. Unfortunately, I found only one van der Waals potential and one cutoff can be defined in .mdp file of one run. Did I miss some features of GR

[gmx-users] Re Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?

Thanks, David. Let me simplify my system. It includes A and B molecules. The van der Waals interaction between A's is, e.g. U1(r) = -1/r cutted off at r = r_A ; and for B: U2(r) = -1/r^2, cut off at r = r_B. I don't know how to handle with two potentials and two cutoffs simultaneously. --

回复： [gmx-users] Re Can GROMACs use mult iple van der Waals potentials and multiple va n der Waals potential cutoffs?

Waals interactions. On 2010-03-31 21.53, hong bingbing wrote: > Thanks, David. > > Let me simplify my system. It includes A and B molecules. The van der > Waals interaction between A's is, e.g. U1(r) = -1/r cutted off at r = > r_A ; and for B: U2(r) = -1/r^2, cut off at r = r_B. >

回复： 回复： [gmx-users] Re Can GROMACs use multiple van der Waals potentials and multipl e van der Waals potential cutoffs?

, 2010 at 5:31 PM, hong bingbing wrote: > >Thanks. But I've read the manual. It seems not solving it. The two potentials >in my system are of totally different function forms. They do not just differ >in the parameters. What troubles me is GROMACS seems not to be able to suppo

[gmx-users] Virial and Pressure

Hi, everyone, Just ask if my interpretation is correct. Does the virial for pressure calculation include all kinds of interactions, non-bonded and bonded? Is there a way to self-defined virial with only specified interaction components? Thank you Bingster -- gmx-users mailing list