Hi Gangotri,
You can increase the force constant.
Best, -Yu
2017-07-19 19:15 GMT+01:00 gangotri dey :
> Hello all,
>
> I am a relatively new user of gromacs. Hence, I am encountering some
> problem.
>
> I am studying few drug molecules onto a metal oxide surface. I would like
> to constrain the R
Hi Mark,
Great! Thanks a lot. I try with the g96 format.
Best, -Yu
2017-06-15 15:04 GMT+01:00 Mark Abraham :
> Hi,
>
> Yes g96 is a good format for that
>
> Mark
>
> On Thu, 15 Jun 2017 14:38 Yu Ogawa wrote:
>
> > Hi Mark,
> > Thanks for suggestions. I will
e trying to do. That would have been
> good to describe, rather than assuming the form of the solution ;-)
>
> Mark
>
> On Thu, 15 Jun 2017 13:10 Yu Ogawa wrote:
>
> > Hi Eric,
> > Thanks for replying.
> >
> > I may be wrong, but what I understand from
>
> As far as I know, Gromacs will accept gro files with high precision if the
> input file follows this format.
>
> Best,
> Eric
>
> > On Jun 15, 2017, at 4:33 AM, Yu Ogawa wrote:
> >
> > Hello gmx users,
> > Can we increase a precision of input structure
Hello gmx users,
Can we increase a precision of input structure file more than 3 decimal
places?
Thank you for your help!
Yu
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ws for an optional data file
> input "nsfactor.dat" but am unsure what that does. Could you provide some
> details into what exactly goes into the "nsfactor.dat" file and what the
> output would be? Thanks for your help.
>
> Regards,
>
> Evan L.
> On
Hi Evan,
I had the same issue, and could not solve the problem as I did not go into
the source code.
What I did at that time is to use "gmx sans" with modified nsfactor.dat
where I put atomic number instead of scattering length, though I don't know
how appropriate that approach is..
Yu
2016-07-0
Hi Stéphane,
gmx gangle may be what you need.
http://manual.gromacs.org/programs/gmx-gangle.html
-Yu
2016-05-31 13:22 GMT+02:00 ABEL Stephane 175950 :
> Hi all,
>
> Is there a command/tool in a gromacs to compute the angle between a vector
> defined defined two atoms molecule and the normal to a
Hi,
I am not an expert, but I think there is no such tricky parameter for
normal mode calculation though I don't know what your situation is..
You can find some tips at the below link..
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
If you set parameters extremely wrong the grom
Dear Justin,
Thank you very much for your advice.
Okay, I will try according to your procedure.
Yu
2014-05-23 19:48 GMT+02:00 Justin Lemkul :
>
>
> On 5/23/14, 1:26 PM, Yu Ogawa wrote:
>
>> This is my mdp file.
>>
>> ;define = -DFLEX_SPC
DispCorr= EnerPres
optimize_fft= yes
2014-05-23 19:07 GMT+02:00 Justin Lemkul :
>
>
> On 5/23/14, 1:02 PM, Yu Ogawa wrote:
>
>> Sorry for my poor explanation. I tried to simulate a temperature rising
>> process from 0 K to 500 K.
>> At first I did a s
> >
> >
> > 2014-05-23 16:33 GMT+02:00 Mark Abraham :
> >
> > > First, find something out. Does the installation work for any other
> > > simulation? What does the log file say? Have you equilibrated your
> system
> > > first? Does another integr
rk?
>
> Mark
>
>
> On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa wrote:
>
> > Hello gmx-users,
> >
> > I tried to run a simulation to calculate a specific heat capacity of
> > infinite molecular crystal with the md-vv integrator and Nose-Hoover
> > thermos
good ideas for this problems?
I would appreciate very much if somebody gives any comments on this matter.
Thank you,
Yu
Yu OGAWA, PhD
Cermav-CNRS, Grenoble, France
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