In addition to others' suggestions, you also have the option of writing /
converting to .gro, which already has flexible precision for the coordinate
fields. Use the -prec output option if needed.
Mark
On Mar 18, 2014 12:00 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/17/14, 6:45 PM, Andrew
dear all,
i performed a simple test for free energy calculations
turning off one water molecule to determine the
chemical potential of water.
I start from a well equilibrated water box. At lambda=1.0
(the fully coupled state) the simulation stops and dies at the
first step without any error
Thank you very much for the information.
Would CHL1 CHARMM-Gromacs porting imply just reformatting the lines of CHL1
(with preservation of all the point charge values) of CHARMM into
appropriate Gromacs lines for charmm36? If this is the case could you please
comment whether the following CHL1 in
Forgot to mention that the atom and type namings are also preserved across
CHARMM - Gromacs.
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Thank you very much.
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figured it out ... the new soft core thingy (48-1) does not
seem to be very stable at single precision ...
if i use
sc-alpha = 0.5
sc-r-power = 6
instead of
sc-alpha = 0.002
sc-r-power = 48
it seems to work
this has in fact been
Hi All,
To follow up on a few recent issues that we have discovered and/or have been
reported here, we have updated our CHARMM36 force field files. As always, they
can be downloaded from:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
Here is a list of changes:
1. An error in
You can get most of these tabulated in a CRC book, an older one is easier to read (circa 1988), online through the international union of physics and chemsitry web site(s), or look over the partial force field (54a7) and locate the same bonds/angles such as aminos and nucleic acids, as the
Dear Justin,
Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn
bound to H2O (water) in updated CHARMM36 ff? For example, this state is
important for some structures. E.g. Carbonic anhydrase.
Ahmet Yıldırım
18 Mar 2014 tarihinde 18:44 saatinde, Justin Lemkul
On 3/18/14, 1:32 PM, Gmail2 wrote:
Dear Justin,
Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn
bound to H2O (water) in updated CHARMM36 ff? For example, this state is
important for some structures. E.g. Carbonic anhydrase.
No. We don't have any special
My colleague and I have simulated atomistic polymers containing PEG. If the
issue is just parameters, you can find them here:
http://pubs.rsc.org/en/content/articlelanding/2010/sm/c001988g#!divAbstract
From:
If you can think of a sensible way to define your area of interest, a
simple VMD script can count waters:
[atomselect mol ID name \O.*\ and resname water resname and same
residue as define area somehow frame frame] num
e.g. To count the number of water molecules within 5A of residues 1-5:
Dear all,
I want to calculate cavity size inside some liquid in which CO2 is
dissolved. Can somebody help me?
Thanks.
PRAVEEN KUMAR
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