, Szilárd Páll szilard.p...@cbr.su.se wrote:
On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan shraba...@gmail.com wrote:
Dear All,
I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with
-DGMX_MPI=ON . I am assuming as OPENMP is default, it will be
automatically installed.
My Compiler is
/opt
, Aug 27, 2012 at 6:25 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 28/08/2012 2:33 AM, jesmin jahan wrote:
Dear All,
I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I
am not interested to any other energy terms right now, I have set all
the non-bonded parameters
,
Jesmin
On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul jalem...@vt.edu wrote:
On 8/29/12 11:11 AM, jesmin jahan wrote:
Thanks Mark for your reply.
For the time being, I admit your claim that I am comparing apple with
orange.
So, to investigate more, I run the simulation without any
...@vt.edu wrote:
On 8/29/12 11:27 AM, jesmin jahan wrote:
Ops!
Thanks Justin for you quick reply.
Sorry, I have attached a log file from previous run. I am attaching
the correct log file here. Please have a look.
I don't see a new .log file attached anywhere.
Actually, I am a Computer
at 1:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/29/12 1:06 PM, jesmin jahan wrote:
Dear Justin,
Thanks for your reply.
Here is the CMV.log file . Please check it.
What you've posted is output from grompp. Note that if you're trying to
send attachments, the list rejects them
knows about this, please let me know.
Thanks for help.
Best Regards,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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about this, please let me know.
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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in each of those
processes /nodes because there is no mention about the number of
threads.
Does anyone know about this?
Sincerely.
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
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Okay Mark, Thanks!.
Best Regards,
Jesmin
On Mon, Aug 27, 2012 at 6:15 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 28/08/2012 2:40 AM, jesmin jahan wrote:
Dear Gromacs Users,
I have two questions about the multi-level parallelism of Gromacs.
http://www.gromacs.org/Documentation
+050.0e+00
If anyone has ever experienced this kind of problem, or knows the
solution, please let me know. Thanks in advance.
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
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implicit_solvent= GBSA
gb_algorithm= OBC ; Still
sa_algorithm= None
Thanks,
Jesmin
On Sat, Aug 25, 2012 at 11:25 AM, Justin Lemkul jalem...@vt.edu wrote:
On 8/25/12 10:57 AM, jesmin jahan wrote:
Dear all,
I got the following error while running mdrun-gpu, I got
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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/install-mdrun.dir/rule] Error 2
make: *** [install-mdrun] Error 2
Is there anyone out there who has faced the same kind of problem and
know the solution?
Any kind of help will be highly appreciated.
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
gmx
/libOpenMM.so)
Can anyone help me to about how to solve this problem?
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
gmx-users mailing listgmx-users@gromacs.org
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of Gromacs which supports implicit solvent
simulation on GPU? Please let me know.
Thanks,
Jesmin
On Tue, Aug 21, 2012 at 4:24 PM, Szilárd Páll szilard.p...@cbr.su.se wrote:
Dear Jesmin,
On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan shraba...@gmail.com wrote:
Dear All,
I have
for gromacs?
Thanks,
Jesmin
On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 17/08/2012 1:14 PM, jesmin jahan wrote:
Hi Mark,
According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles
Okay thanks. I got it. :-)
Best Regards,
Jesmin
On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote:
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So
) from gromacs simutation?
Thanks,
Jesmin
On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan shraba...@gmail.com wrote:
Thanks Mark for your reply. I was trying to use Single-Point Energy
Calculation as you advised in your first reply but for most of the
files the simulation failed because I
values are?
That's why time is an important factor me my experiments and I really
want to measure the time for GB energy in isolation !
Thanks,
Jesmin
On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/08/2012 4:26 PM, jesmin jahan wrote:
Hi Mark,
Thanks
mark.abra...@anu.edu.au wrote:
On 16/08/2012 5:08 PM, jesmin jahan wrote:
Hi Mark,
Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?
In the .top file from which you made
, Aug 14, 2012 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/08/2012 7:38 AM, jesmin jahan wrote:
Dear Gromacs Users,
I have some questions regarding GB-Polarization Energy Calculation
with Gromacs. I will be grateful if someone can help me with the
answers.
I am trying
. Is there any known speedup factor of Gromacs on multicores?
Thanks for your help.
Best Regards,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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in gromacs?
3. Can I only calculate the GB-polarization energy without calculating
any Forces? How?
4. What are the good tools to get the GB- energy values along with the
time to calculate the GB-energy?
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
gmx-users
Hi Mark,
Thanks for your reply. I will try to follow your instructions.
Thanks,
Jesmin
On Thu, Aug 9, 2012 at 9:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 10/08/2012 3:06 AM, jesmin jahan wrote:
Dear Gromacs Users,
I am a new user of Gromacs and I am using gromacs to calculate
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