If diff says there are no changes, then you're not comparing with the file
you changed...
On Sep 25, 2013 1:59 PM, "shahab shariati"
wrote:
> Dear Mark
>
> > The UNIX tool diff is your friend for comparing files.
>
> Thanks for your suggestion. I used diff and sdiff toll
> for comparing 2 files (
Dear Mark
> The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for comparing 2 files (before and after correction).
diff old.gro new.gro
These tolls did not give me any output file or text
containing difference between 2 files.
In this
The UNIX tool diff is your friend for comparing files.
On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati
wrote:
> Dear Tsjerk
>
> Thanks for your reply
>
> Before correcting the gro file, I knew that gro file is fixed format.
> I did this correction very carefully.
>
> Part of the gro file before
Dear Tsjerk
Thanks for your reply
Before correcting the gro file, I knew that gro file is fixed format.
I did this correction very carefully.
Part of the gro file before and after correction is as follows:
-
before:
---
Dear Tsjerk
Thanks for your consideration.
I ignored Warning 1.
> WARNING 1 [file topol.top, line 32]:
> 3632 non-matching atom names
> atom names from topol.top will be used
> atom names from system.gro will be ignored
Based on your suggestion, I checked non-matching
atom names between t
Hi Shahab,
You edited the .gro file, but you made an error. So you have to read the
manual to understand the file format and then see where and how your edited
file doesn't match.
Cheers,
Tsjerk
On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati
wrote:
> Dear Tsjerk
>
> Thanks for your consider
Hi Shahab,
That site has a lot of structures. It would be better to explicitly state
which one you took. However, in this case, the better question is, how did
you write the topology, and did you check the correspondence of the order
of molecules/atoms in the topology file and the structure file?
Dear Tsjerk
Thanks for your consideration.
My system contains 2 components: (DOPC & cholesterol) lipids + water
molecules.
I get force field parameters from lipid book (for dopc and cholesterol).
I used input coordinate file (system.gro) from following web site:
http://people.su.se/~jjm/Stockh
Hi Shahab,
What did you do exactly? Can you state your complete protocol (1. fetched
this structure file there, 2. got the topology from there, 3. did
something, 4. ran grompp like this, etc)? Use brief, clear explanations and
the command lines as you issued them.
Cheers,
Tsjerk
On Tue, Sep 17
On 9/17/13 8:47 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
I am very confused and amazed.
After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.
Any help will highly appreciated.
I honestly have no idea.
Dear Justin
Very very thanks for your quick reply.
I am very confused and amazed.
After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.
Any help will highly appreciated.
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On 9/17/13 8:17 AM, shahab shariati wrote:
Dear Justin
Thanks for your time and consideration.
As I suggested before, visualize the output file and figure out what is
around atom 618 to cause such forces.
I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc
molecule (t
Dear Justin
Thanks for your time and consideration.
> As I suggested before, visualize the output file and figure out what is
> around atom 618 to cause such forces.
I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc
molecule (this dopc molecule is intact and is not broken
On 9/17/13 7:02 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply
You're still working with outdated software. Please follow my
suggestion of trying 4.6.3.
I try to install 4.6.3.
The larger issue, in the end, is the unphysical configuration of the drug
in the membrane. Ind
Dear Justin
Thanks for your reply
> You're still working with outdated software. Please follow my
> suggestion of trying 4.6.3.
I try to install 4.6.3.
> The larger issue, in the end, is the unphysical configuration of the drug
> in the membrane. Independent of Gromacs version, that setup wi
On 9/17/13 5:03 AM, shahab shariati wrote:
Dear Justin
I used newer version of gromacs (4.6.1), but my problem was not solved.
You're still working with outdated software. Please follow my suggestion of
trying 4.6.3. The larger issue, in the end, is the unphysical configuration of
the d
Dear Justin
I used newer version of gromacs (4.6.1), but my problem was not solved.
Any help will highly appreciated.
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Dear Justin
Very very thanks for your quick reply.
> The sys.gro file is positioned within a box that is too large, a fact that is
> easily observable in VMD. I suspect that the void space results in
> instability.
If I positioned system in a smaller box, my problem (instability) solved ???
On 9/16/13 10:52 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
The sys.gro file is positioned within a box that is too large, a fact that is
easily observable in VMD. I suspect that the void space results in instability.
If I positioned system in a smaller
Dear Justin
Very very thanks for your quick reply.
> The sys.gro file is positioned within a box that is too large, a fact that is
> easily observable in VMD. I suspect that the void space results in
> instability.
If I positioned system in a smaller box, my problem (instability) solved ???
On 9/16/13 9:47 AM, shahab shariati wrote:
Dear Justin
My input coordinate file is a gro file (sys.gro). When I visualize that by VMD,
all things is ok and true.
After minimization, I obtained a gro file (em.gro). When I visualize that by
VMD, About 5 DOPC molecules leave bilayer structure an
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