xiaowu759 wrote:
Dear gmxers,
While performing EM using GMX, I find in the resullting gro file,
residues and atoms are reordered. Do this affect the simulation? Please
give me some hints. Thanks a lot!
Before EM，gro file:
1 HmP ..
2 HmP ..
.
20 MmP ...
21 MmP ..
Dear gmxers,
While performing EM using GMX, I find in the resullting gro file, residues and
atoms are reordered. Do this affect the simulation? Please give me some hints.
Thanks a lot!
Before EM，gro file:
1 HmP ..
2 HmP ..
.
20 MmP ...
21 MmP ..
.
thumbs up per tuti
On Jul 15, 2011, at 6:23 PM, Justin A. Lemkul wrote:
Sara baretller wrote:
between 2.2 and 2.7 M.
Well, double check your work. Your previous post contained several
units that made no sense, so I don't know if you've done the
calculations correctly. For adding ions,
Sara baretller wrote:
between 2.2 and 2.7 M.
Well, double check your work. Your previous post contained several units that
made no sense, so I don't know if you've done the calculations correctly. For
adding ions, just use genion -conc and it will do the work for you. That way,
you'll
between 2.2 and 2.7 M.
Thank you
On Fri, Jul 15, 2011 at 5:40 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> thank you for your help, will it be alot to add 700 ions to a system made
>> of water and proteins that is 4000 molecules
>>
>
> That would certainly be an extraordinaril
Sara baretller wrote:
thank you for your help, will it be alot to add 700 ions to a system
made of water and proteins that is 4000 molecules
That would certainly be an extraordinarily high concentration. What is your
target molarity?
-Justin
--
J
thank you for your help, will it be alot to add 700 ions to a system made of
water and proteins that is 4000 molecules
--
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Seibold, Stephen wrote:
I am sorry if this is a simple question, but I have spent the better
part of the day attempting to figure it out using gromacs mailing
list..etc..
Here is the problem. When I attempt to run genbox my output produces the
error that "spc216.gro cannot be found in your
I am sorry if this is a simple question, but I have spent the better part of
the day attempting to figure it out using gromacs mailing list..etc..
Here is the problem. When I attempt to run genbox my output produces the error
that "spc216.gro cannot be found in your GMXLIB path. Here is what I'v
Thanks Baofu. It seems that my topology file indeed is missing bonds
for the sidechains! I am using a webtool so I am wondering whether
the tool does not support these residues.
> are you sure that your topology file is correctly written?
On 07/15/2011 11:34 AM, Zack Scholl wrote:
> Hi all -
>
Sara baretller wrote:
yes
i had X M and i convert it to X molecule / mol using Avogadro's number.
but how do i get only molecules or ions
I'm not following your notation. If you've got a given concentration (mol/L),
you obtain molecules/L by using Avogadro's number. Then just multiply
yes
i had X M and i convert it to X molecule / mol using Avogadro's number. but
how do i get only molecules or ions
On Fri, Jul 15, 2011 at 1:52 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi All
>>
>> I have a question about adding ions to the system. using Genion one can
>>
Sara baretller wrote:
Hi All
I have a question about adding ions to the system. using Genion one can
add ions but how can you convert molecule/mol to number of molecules or
ions ??
let say 2 e 23 molecule/mol to X number of molecule or ions
Use Avogadro's number.
-Justin
--
==
Hi All
I have a question about adding ions to the system. using Genion one can add
ions but how can you convert molecule/mol to number of molecules or ions ??
let say 2 e 23 molecule/mol to X number of molecule or ions
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/m
There might be relevant to walltime settings. There might be a default limit.
try qsub -l walltime=1000:00:00 yourjob
adjust the time or google further to meet your need.
On Fri, Jul 15, 2011 at 2:27 AM, Justin A. Lemkul wrote:
>
>
> Sayan Bagchi wrote:
>>
>> Hello All,
>> I am having a weird
Hi,
have look to the orient package for vmd:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
In the vmd script repository there is also a python script:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fit_angle/
I have done a script using orient which calculate th
There must be several tools to calculate the angle between two domains
connected at a hinge. I was wondering if someone has suggestions on any
tools, or whether it is possible to do this using a vmd plugin directly for
a trajectory? IN my case, I have a reasonable good idea where the hinge is.
I wa
On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote:
Hello,
I am trying to evaluate energy values of several conformations using a
(pseudo)trajectory. Currently, I am concatenating GROMOS-96 files
(.g96) and using that as a trajectory. For some reason the second
conformation in a trajectory is ig
are you sure that your topology file is correctly written?
On 07/15/2011 11:34 AM, Zack Scholl wrote:
Hi all -
I'm running a simulation that has an implicit solvent. I ran my
simulation and it seems that everything not connected to the backbone
has floated off into space. Is there a way to de
Hi all -
I'm running a simulation that has an implicit solvent. I ran my
simulation and it seems that everything not connected to the backbone
has floated off into space. Is there a way to define connections so
that side chains stay connected? Has anyone had this problem before?
Thanks,
Since
Hello,
I am trying to evaluate energy values of several conformations using a
(pseudo)trajectory. Currently, I am concatenating GROMOS-96 files (.g96) and
using that as a trajectory. For some reason the second conformation in a
trajectory is ignored. So e.g. if I have three conformations (1.g96, 2
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