Dear Mark,
Thank you for your reply. Unfortunately, TIP5P is completely rigid and
the FLEXIBLE define will not change it. Any other ideas?
Best,
g
On 2013-09-24 23:51, Mark Abraham wrote:
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a fle
On 9/24/13 2:40 PM, fatemeh ramezani wrote:
Dear Justin
I'm simulating gold nanoparticle interaction with protein by OPLSAA
forcefield. I'm confused for selection an ensemble for my md run. I did
energy minimization by NPT . then I did the MD by NVT. I did it because of
Let's take a step b
On 9/24/13 7:16 AM, aixintiankong wrote:
Dear prof.
The format of parameters is convenient to the software of Amber and
not to gromacs. if i use the parameters i must use some tools to convert it to
the itp format for gromacs. so i use acpype to get itp format.
i just doubt th
On 9/23/13 11:43 PM, Santhosh Kumar Nagarajan wrote:
Justin..
I understand the problem..
But.. How to generate a .rtp file myself..
Study existing examples, read manual section 5.6.1, and fire up a text editor.
-Justin
--
==
Justin A. Lemkul
Ok, thanks, I may just do that
On Tue, Sep 24, 2013 at 2:42 PM, Mark Abraham wrote:
> The FF+water combinations still work the same way they did 3 years
> ago! :-) The important question is whether validation for the
> observables has occurred. (And no relevant problems were seen). If the
> pape
The FF+water combinations still work the same way they did 3 years
ago! :-) The important question is whether validation for the
observables has occurred. (And no relevant problems were seen). If the
paper does not support its decision to mix and match, go and ask them
why it was reasonable!
Mark
Dear all,
I have been trying to evaluate a paper that used amber99 with SPC water to
simulate a protein. How would this affect the results, is it important? I
googled for a bit, all I found was:
"Amber, charmm and OPLS-AA were developed with TIP3P, and that should be
the default. Except that charm
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a flexible molecule, e.g. define
= -DFLEXIBLE (or something). Check your water .itp file for how to do
it.
Mark
On Tue, Sep 24, 2013 at 10:25 PM, gigo wrote:
> Dear GMXers,
> Since I am intereste
Dear GMXers,
Since I am interested in interactions of lone electron pairs of water
oxygen within the active site of an enzyme that I work on, I decided to
give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to
minimize freshly solvated system. I found on the gmx-users
(http:/
Hello,
On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy wrote:
> I have been using the new tool "gmx gangle". My actual intention is to
> calculate the orientation between any two same molecules (say cholesterol)
> throughout the trajectory and there are 40 cholesterol molecules. But I
> couldn't c
Dear Justin
I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield.
I'm confused for selection an ensemble for my md run. I did energy minimization
by NPT . then I did the MD by NVT. I did it because of studying of two paper
that were similar to my project (Adsorption
Dear all,
I have sent this e-mail to the gmx-users mailing list for a few days, but
without any reply until now. I'm not sure if it has something to do with the
format, because the link can’t be opened when I search the mailing list. So
this time I use the plain text and send it once more, wou
Dear all,
I have sent this e-mail to the gmx-users mailing list for a few days, but without any reply until now. I'm not sure if it has something to do with the format, because the link can’t be opened when I search the mailing list. So this time I use the plain text and send it once more, would a
Dear list members,
I am trying to simulate an infinite layer of quartz in Gromacs. Due to my
needs (afterwards I need to place a large molecule on top of it) the surface
must be at least 12x12 nm^2. I generated the input files from a pdb file of
the structure, and adapted the OPLS force field to m
Dear prof.
The format of parameters is convenient to the software of Amber and not
to gromacs. if i use the parameters i must use some tools to convert it to the
itp format for gromacs. so i use acpype to get itp format.
i just doubt that i use amber99sb for protein and AM1-BBC for
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