All of the Charmm force field parameters may be found on Alex
MacKerell's website: http://mackerell.umaryland.edu/
CHARMM_ff_params.html. Converting from Charmm units and potential
form to Gromacs is straightforward.
Andrew
On Dec 7, 2011, at 12:59 PM, Michael McGovern wrote:
Hi everyone.
I believe your problem is that you do not understand scientific notation.
5.70e+01 = 57. Cl- has a charge of -1. Need I say more.
On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia
wrote:
> Hi,
>
> The genion command i used is
> genion -s genion.tpr -o ago_water_ions.gro -nn 6
>
> I used this t
, Andrew Paluch wrote:
The LJ interaction is 0. But you're asking about a bond. 1-2
interactions are typically modeled with a harmonic potential. This
is most
definitely not zero.
On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote:
If eplilon of hydrogen atom is zero then the lennard
The LJ interaction is 0. But you're asking about a bond. 1-2
interactions are typically modeled with a harmonic potential. This is
most definitely not zero.
On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote:
If eplilon of hydrogen atom is zero then the lennard jones
interaction of
OH bond
You can calculate that by hand on a calculator in a few seconds.
There is no need to use Gromacs.
On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote:
Hello,
How can I calculate Lennard Jones interaction for two selected
atoms with
a specific distance?
I am using Gromacs 4.0.7 version.
Tha
There is no error. The alkane dihedral parameters were updated in 1999, and
differ from those originally published in 1996.
Andrew
On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S wrote:
> Hi all,
>
> Hi
>
>
>
> I've converted the OPLS-AA torsional potential parameters for the
>
> alkane C-C-C-C (C
If you get this to work, you may still have problems as SPC and TIP3P
have different geometries. A box of 216 waters is pretty easy to
equilibrate; you could have this done for TIP3P in no time at all.
On Apr 16, 2010, at 4:46 AM, kecy...@sina.com wrote:
Hello,I want to use spc216.gro an
Read the manual. You can explicitly declare all of your cross terms rather
than using the same mixing rule for all terms. You can easily write a
script to modify your input files accordingly,
Andrew
On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari wrote:
> Hi All,
>
> Recently there has been a ne
interested in, you may have better
luck with a water model other than TIP3P.
Hope this helps,
Andrew
___
_______
Andrew Paluch
Department of Chemical and Biomolecular Engineering
University of Notre Dame du Lac
Does anyone know of a reference (besides the manual) for the
calculations performed by g_current?
Thank you,
Andrew
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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You can either specify this explicitly or use the fudge LJ and fudge
q headers in your topology file. See the manual for details.
On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote:
Hi,
Is it possible in gromacs to make 1-4 interaction energy reduced as
compared to the intermolecular inter
run-time flags that
I should be using?
Thank you,
Andrew
___
___
Andrew Paluch
Department of Chemical and Biomolecular Engineering
University of Notre Dame du Lac
apal...@nd.edu
To whom this may concern,
I am receiving the following errors when attempting to run Gromacs in
parallel:
Making 1D domain decomposition 4 x 1 x 1
p2_21562: p4_error: Timeout in establishing connection to remote process: 0
p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32
wh
To whom this may concern,
Is it possible to use FudgeLJ to scale 1-4 interactions when using a
Buckingham Potential? Also, are long range corrections implemented
for the Buckingham Potential?
Thank you,
Andrew
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