Jack Shultz wrote:
I am trying to run g_dist
c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr
---
Program g_dist, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
index.ndx
--
Jack Shultz wrote:
I am trying to run g_dist
c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr
---
Program g_dist, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
index.ndx
I am trying to run g_dist
c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr
---
Program g_dist, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
index.ndx
-
Darrell Koskinen wrote:
Hi Mark,
No, I am not trying to build a random number generator and hope that I
am not moving in this direction : )
My definition of adsorption energy would be the difference in energy
when two species are at an infinite distance and the energy when these
species are
ms wrote:
Hi,
I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informati
Hi Mark,
No, I am not trying to build a random number generator and hope that I
am not moving in this direction : )
My definition of adsorption energy would be the difference in energy
when two species are at an infinite distance and the energy when these
species are at an equilibrium distanc
Darrell Koskinen wrote:
Thanks for the additional comments.
So given that, in my system, I have H atoms attached to C atoms on the
perimeter of a finite graphene sheet that is placed above multiple
infinite layers of graphene (graphite), would it be more appropriate to
use: (i) a classical
Thanks for the additional comments.
So given that, in my system, I have H atoms attached to C atoms on the
perimeter of a finite graphene sheet that is placed above multiple infinite
layers of graphene (graphite), would it be more appropriate to use: (i) a
classical (harmonic) model using cons
Dear all,
I have a covalently bond ligand to a protein which its c=c bond could stay
in Cis-enamine or Trans-enamine (I relaxed the structures of those two using
classical MD in Gromacs4). I'm calculating the free energy difference of the
Cis and Trans states using thermodynamic integration impleme
Hi,
I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informative. Thanks!
Hi Rasmus,
>From your previous email I understood that you have only two molecules
(you didn't write that you're using 500 and nothing on the rest of the
system). Apparently, this is not the case. I don't think you can get
what you want from g_hbond without modifying the source code. If you
don't
Hi Ran.
If I understand you right, then you suggest to have one molecule as
acceptor, and the rest (499) as donors, and then look in the hbnum.xvg
to see how often there is two hydrogen bonds...
1. is that I have to do this check for every molecule.
2. there is no guaranty that the two hydro
Hi Rasmus,
A simple solution would be to run g_hbond twice, with two separate
groups for acetate 1 as donor and acetate 2 as acceptor or vice versa,
check the existence an hydrogen bond with g_hbond -num and write a
script to check when the two hydrogen bonds co-exist.
Hope that helps,
Ran.
Rasm
Hi All.
I'm trying to calculate the Hydrogen bond occupancy when there is two
hydrogen bonds between same two acetic acid molecules at the same time.
With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen
bonds" group and the hbmap.xpm gives me the matrix of when these
hydrogen
Erik Marklund wrote:
> Mark Abraham skrev:
>> Darrell Koskinen wrote:
>>> Hi Tsjerk,
>>> So then, if I understand correctly, setting "constraints =
>>> all-bonds" is not as realistic as setting "constraints = none",
>>> since the latter will allow for flexible (e.g. harmonic) behavoir
>>> which is
Antonia V. wrote:
> > I am trying to simulate a two component system, and I would like to
ask
> > you the two following questions:
> >
> > 1) Is it possible to use a different scaling factor (for the LJ and
the
> > electrostatics) for each component?
>
> Not natively. How would you li
Mark Abraham skrev:
Darrell Koskinen wrote:
Hi Tsjerk,
So then, if I understand correctly, setting "constraints = all-bonds"
is not as realistic as setting "constraints = none", since the latter
will allow for flexible (e.g. harmonic) behavoir which is more
realistic than fixing the bond to a
This is exactly what I thought.
I found out that saving the file with .mol ending in PyMol does not give the
unwanted bonds.
Thank you all.
On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman wrote:
> With VMD it's even simpler: use "dynamic bonds".
>
> Ran.
>
> Nicolas Sapay wrote:
> >
> >
> > Dall
> > I am trying to simulate a two component system, and I would like to ask
> > you the two following questions:
> >
> > 1) Is it possible to use a different scaling factor (for the LJ and the
> > electrostatics) for each component?
>
> Not natively. How would you like to treat non-bonded int
Dear all,
I am busy following the EMBO tutorial on membrane proteins
(http://www.dddc.ac.cn/embo04/practicals/9_16.htm) but it is 2 days
now that the server is down. Does anybody maybe know another url where
I can find this tutorial?
Thanks!
Irene
--
gmx-users mailing listgmx-users@gromacs.o
With VMD it's even simpler: use "dynamic bonds".
Ran.
Nicolas Sapay wrote:
>
>
> Dallas B. Warren a écrit :
>>
>> Coordinate files like pdb and gro aren’t used by GROMACS to provide
>> any bonding information. That is what the topology files are for. So
>> their “presence” in your pdb isn’t an is
Dallas B. Warren a écrit :
Coordinate files like pdb and gro aren’t used by GROMACS to provide
any bonding information. That is what the topology files are for. So
their “presence” in your pdb isn’t an issue.
Actually, what is probably happening is that PyMol is guessing the
bonds presenc
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