[gmx-users] Re: gmx-users Digest, Vol 103, Issue 111

[Pruthvi Bejugam]

Thank you so much Dr. Mark,

   If I install the normal version of
Gromacs in my nvidia GPU Tesla M2090, intel quartz core processor, what
would be the difference in performance of Gromacs in terms of speed and
accuracy, when we compare with
GPU version of Gromacs. can you suggest me how can i improve the
performance in that GPU (Even though i install a Normal version of
Gromacs). Any suggestions or help would be highly appreciated.


Thank you again.

--
>
>
> Message: 6
> Date: Fri, 23 Nov 2012 16:27:15 +0100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Query about GPU version of Gromacs
> To: Discussion list for GROMACS users 
> Message-ID:
>  fwkrykicio...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> The GPU functionality available in GROMACS 4.5 based on OpenMM is likely to
> be deprecated because we lack the resources to continue to support it - as
> you can see from the limited documentation you can see for it on our
> website. I would advise against attempting to build or use anything other
> than an official GROMACS release.
>
> The good news is that the upcoming GROMACS 4.6 release will have native GPU
> support for a much larger range of algorithms than have been available
> previously. Unfortunately, we still can't provide a timeline for that
> release yet. Portability, reliability, high performance and rapid
> time-to-market tend to be mutually exclusive, I'm afraid!
>
> Mark
>
> On Fri, Nov 23, 2012 at 10:53 AM, Pruthvi Bejugam  >wrote:
>
> > Hai all,
> >
> >Can any body suggest me which is most stable version of
> > GPU-GROMCS. and as far as Gromacs site is concerned currently all the
> > versions are unstable. If there is no stable version for GPU is available
> > then when would a stable version for GPU would be released.
> >
> > and another query is when i was compiling this
> >
> > gromacs-4.5-GPU-beta2_linux-X86_64.tar.gz (Unstable)
> >
> >  GPU version of Gromacs i get path error where it is showing that gcc
> > compiler is not at the
> > given path even though path for all the gcc compilers remains the same.
> >
> > any suggestions would be greatly appreciated.
> >
> > Thank you,
> >
> > --
> > PruthviRaj Bejugam,
> > Junior Research Fellow,
> > Lab. No.9 (New Building)
> > Computational and Systems Biology Lab,
> > National Centre for Cell Science,
> > Ganeshkhindh, Pune, INDIA 411007
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] force vs time plot

[Paula Andrea Delgado Pinzon]

Hi to all gromacs users,

I am trying to run an umbrella sampling and i am getting the initial 
conformations by pulling simulations but i want to check the simulation through 
the force vs time plot to see if my complex did or did not separate, so how can 
i get this plot?

Thank you for your time

Paula


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Group selection for the output in trjconv command

[Shima Arasteh]

Hi all,

When I run the trjconv , it asks me to select the group for the output. 

I want to invade the group selection into the trjconv command. How would it be 
possible? In fact I don't want to select the group manually, I want it to be 
done automatically and no questions about group selection appears on the screen.

Thanks for your suggestions.
Sincerely,
Shima 
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] force vs time plot

[Justin Lemkul]

On 11/24/12 7:09 AM, Paula Andrea Delgado Pinzon wrote:

Hi to all gromacs users,

I am trying to run an umbrella sampling and i am getting the initial 
conformations by pulling simulations but i want to check the simulation through 
the force vs time plot to see if my complex did or did not separate, so how can 
i get this plot?



That is what the pullf.xvg file contains.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Group selection for the output in trjconv command

[Justin Lemkul]

On 11/24/12 7:11 AM, Shima Arasteh wrote:



Hi all,

When I run the trjconv , it asks me to select the group for the output.

I want to invade the group selection into the trjconv command. How would it be 
possible? In fact I don't want to select the group manually, I want it to be 
done automatically and no questions about group selection appears on the screen.



http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] On the usage of SD integrator as the thermostat

[Krzysztof Murzyn]

I am wondering what you mean by 'proper dynamics', Chris? And in
general, what's the advantage of using sd integrator over md
integrator together with Nose-Hoover thermostat.

Thanks,
km.

On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale
 wrote:
> I use the SD integrator with tau_t = 1.0 ps for all of my work, including 
> proteins in aqueous solution
> or embedded in a lipid membrane.
>
> Any value of tau-t is "correct", and none will give you the proper dynamics, 
> but I find that the diffusion of
> both water and lipids is quite reasonable when using tau_t=1.0 ps.
>
> I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest 
> that you search out those old posts.
>
> Chris.
>
> -- original message --
>
> In manual I've found possibility of the usage of the sd (langeven's
> dynamics) integrator as the thermostat.
>
> It's known that friction coefficient in the Langeven's equations is
> defined as m/Tau_t. So the  high values of tau t can be appropriate
> for the modeling of the thermostat without t_coupl. Also I know that
> friction coefficient for such simulation must  corresponds to the
> viscosity of the system.  In Gromacs manual I've found that Tau-t= 2.0
> ps can be appropriate value for such simulations. Does this value
> suitable for water-soluble system only ? What Tau_t should I use for
> modeling of the membrane proteins in the lipid-water environment which
> has higher viscosity ?
>
>
> Thanks for help,
>
> James
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] shall we use Charmm_t3p water model?

[Albert]

hello:

  I found that some people use CHARMM27+t3p for their simulation 
system, and some prefer CHARMM27+charmm_t3p. I am just wondering is it 
necessary to use CHARMM_T3P model for a system which introduce CHARMM FF 
for the protein? I found that it is pretty slow to use CHARMM_T3P model.


thank you very much.
Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] shall we use Charmm_t3p water model?

[Mark Abraham]

Check out the Bjelkmar paper that introduced CHARMM27 into GROMACS, cited
from the manual section about CHARMM (hint, hint)

Mark

On Sat, Nov 24, 2012 at 5:36 PM, Albert  wrote:

> hello:
>
>   I found that some people use CHARMM27+t3p for their simulation system,
> and some prefer CHARMM27+charmm_t3p. I am just wondering is it necessary to
> use CHARMM_T3P model for a system which introduce CHARMM FF for the
> protein? I found that it is pretty slow to use CHARMM_T3P model.
>
> thank you very much.
> Albert
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] shall we use Charmm_t3p water model?

[Albert]

On 11/24/2012 06:29 PM, Mark Abraham wrote:

Check out the Bjelkmar paper that introduced CHARMM27 into GROMACS, cited
from the manual section about CHARMM (hint, hint)

Mark


THX, I found it.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists