On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole wrote:
>
> Really? This is really great!
> Is there any need to specify the location of the vmd libraries?
>
By default it tries to find them at
/usr/local/lib/vmd/plugins/*/molfile
If you have them installed somewhere else you can specify it by s
Daniel L. Ensign wrote:
Hello gmx-users, you rock and rollers,
Equations 4.74 and 4.75 in my copy of the manual have (please pardon my
pseudo-LaTeX):
(4.74)
\phi' = (\phi - \phi_0) MOD 2\pi
(4.75)
V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi' >
\Delta \phi
or
V(\phi
Thanks for the information.
Because of haven't satisfactory model from my co-solvent and I have to add
it randomly along with the solvent by genbox -ci -nmol.
the reason of this criteria relate to crash of system
(solute+co-solvent+solvent) in the first step of simulation, because small
distance b
Hello gmx-users, you rock and rollers,
Equations 4.74 and 4.75 in my copy of the manual have (please pardon
my pseudo-LaTeX):
(4.74)
\phi' = (\phi - \phi_0) MOD 2\pi
(4.75)
V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi' >
\Delta \phi
or
V(\phi') = 0 if \phi' \leq \Del
rasoul nasiri wrote:
Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and
with solutes, i must firstly fill the co-solvents along solutes and
solvents after that i remove solvent, finally by edittconf -translate
the co-solvents uniformally is di
Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and with
solutes, i must firstly fill the co-solvents along solutes and solvents
after that i remove solvent, finally by edittconf -translate the co-solvents
uniformally is distributed in the appropriate
Justin A. Lemkul wrote:
rasoul nasiri wrote:
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between
solutes in simulation box before MD simulation. How can I do it?
You can't. If you know you need a certain distance, that should be part
of your plann
rasoul nasiri wrote:
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between solutes
in simulation box before MD simulation. How can I do it?
You can't. If you know you need a certain distance, that should be part of your
planning :) I suppose you could
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between solutes in
simulation box before MD simulation. How can I do it?
Rasoul
On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul wrote:
>
>
> rasoul nasiri wrote:
>
>> Dear All,
>> Hello
>>
>> I understand one ca
rasoul nasiri wrote:
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by
genbox command and -vdwd but I don't know, how do it between the solutes?
Position your solutes using editconf -center, then add solvent.
-Justin
Thanks for helping!
Rasoul
--
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by genbox
command and -vdwd but I don't know, how do it between the solutes?
Thanks for helping!
Rasoul
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
Really? This is really great!
Is there any need to specify the location of the vmd libraries?
If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this
somehow still possible?
On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote:
In case you use the GIT version of the analysis tools
Bharath.K. Chakravarthi wrote:
hello all...
i know simulating the effect of temperature and pressure on the protein
is there any way to study the effect of Ph on the system
That is a complex question, but there are a number of useful discussions about
this in the list archive. The
Bharath.K. Chakravarthi wrote:
hello all...
when ever i run simulation i'm getting this kind of out put saying there
is one warning
as shown below
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening lib
hello all...
i know simulating the effect of temperature and pressure on the protein
is there any way to study the effect of Ph on the system
--
Bharath.K.Chakravarthi
Ph:9535629260
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pl
hello all...
when ever i run simulation i'm getting this kind of out put saying there is
one warning
as shown below
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gr
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