Re: [gmx-users] Problem with OpenMP+MPI

, then what should be the parameter set? Thanks for your time. Best Regards, Jesmin On Wed, Feb 27, 2013 at 11:54 AM, Justin Lemkul wrote: > > > On 2/27/13 11:27 AM, jesmin jahan wrote: >> >> Thanks again Justin, >> >> I added >> >> cutoff-sche

Re: [gmx-users] Problem with OpenMP+MPI

= protein Best Regards, Jesmin On Wed, Feb 27, 2013 at 10:57 AM, Justin Lemkul wrote: > > > On 2/27/13 10:54 AM, jesmin jahan wrote: >> >> Many thanks to you Justin for your help. >> >> Now my .mdp file looks like: >> >> constraints =

Re: [gmx-users] Problem with OpenMP+MPI

more." Is there any documentation for this? Can I cite you if I want to add this information in an article? Thanks, Jesmin On Wed, Feb 27, 2013 at 10:33 AM, Justin Lemkul wrote: > > > On 2/27/13 10:25 AM, jesmin jahan wrote: >> >> Thanks Justin. >> Well, I am

Re: [gmx-users] Problem with OpenMP+MPI

= protein - Thanks a lot for your help, Jesmin On Wed, Feb 27, 2013 at 10:11 AM, Justin Lemkul wrote: > > > On 2/27/13 10:01 AM, jesmin jahan wrote: &

Re: [gmx-users] Problem with OpenMP+MPI

that I was receiving previously (i.e., -1.58040e+04)? The previous energy was correct, while the current value is 10 times more than the previous one. Thanks, Jesmin On Wed, Feb 27, 2013 at 8:55 AM, Justin Lemkul wrote: > > > On 2/27/13 8:53 AM, jesmin jahan wrote: >> >> Th

Re: [gmx-users] Problem with OpenMP+MPI

Kutzner wrote: > Hi, > > On Feb 27, 2013, at 6:55 AM, jesmin jahan wrote: > >> Dear Gromacs Users, >> >> I am trying to run the following command on gromacs 4.6 >> >> mdrun -ntmpi 2 -ntomp 6 -s imd.tpr >> >> But I am getting the following error

[gmx-users] Problem with OpenMP+MPI

! Thanks, 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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don&#

Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value

Jesmin On Wed, Aug 29, 2012 at 1:11 PM, Justin Lemkul 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 g

[gmx-users] Problem with incorrect GB-Polarization Energy Value

'Protein_chain_C34' Excluding 3 bonded neighbours molecule type 'Protein_chain_A35' Excluding 3 bonded neighbours molecule type 'Protein_chain_B35' Excluding 3 bonded neighbours molecule type 'Protein_chain_C35' ... so on. NOTE 5 [file topol.top, line 388]:

Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value

, Jesmin On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul 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 inves

Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value

ckage. Best Regard, Jesmin On Mon, Aug 27, 2012 at 6:25 PM, Mark Abraham 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

Re: [gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi

, Szilárd Páll wrote: > On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan 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. >> >> M

[gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi

knows about this, please let me know. Thanks for 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 * Please search the archive at http

Re: [gmx-users] Question about Multi-level parallelization: MPI and OpenMP

Okay Mark, Thanks!. Best Regards, Jesmin On Mon, Aug 27, 2012 at 6:15 PM, Mark Abraham 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. >> >&g

[gmx-users] Question about Multi-level parallelization: MPI and OpenMP

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. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Problem with incorrect GB-Polarization Energy Value

about this, please let me know. Thanks, 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 * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!

implicit_solvent= GBSA gb_algorithm= OBC ; Still sa_algorithm= None Thanks, Jesmin On Sat, Aug 25, 2012 at 11:25 AM, Justin Lemkul wrote: > > > On 8/25/12 10:57 AM, jesmin jahan wrote: >> >> Dear all, >> I got the following error while running mdr

[gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!

-2.22432e+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. -- gmx-users mailing listgmx-users@gromac

[gmx-users] Problem with "The requested platform "CUDA" could not be found"

se reply me. Thanks, 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/S

[gmx-users] Problem with Gromacs 4.6 installation

or 2 make[1]: *** [src/kernel/CMakeFiles/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 S

Re: [gmx-users] Problem with Gromacs installation with GPU.

there any version 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 wrote: > > Dear Jesmin, > > On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan wrote: > > Dear All, > > > > I ha

[gmx-users] Problem with Gromacs installation with GPU.

/01945/jesmin/Gromacs/4.5.3/openmm/lib/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 http://lists.gromacs.org/mailman/listinfo/gm

Re: [gmx-users] Questions regarding Polarization Energy Calculation

Okay thanks. I got it. :-) Best Regards, Jesmin On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham wrote: > On 18/08/12, *jesmin jahan * wrote: >> >> Hi Mark, >> >> Thanks for your reply. >> >> In the ffnonbonded.itp, I set all sigma and epsilon values to z

Re: [gmx-users] Questions regarding Polarization Energy Calculation

gromacs? Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham 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

Re: [gmx-users] Questions regarding Polarization Energy Calculation

7 AM, Mark Abraham 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? &g

Re: [gmx-users] Questions regarding Polarization Energy Calculation

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 wrote: >> >> On 16/08/2012 4:26 PM, jesmin jahan wrote: >>> >

Re: [gmx-users] Questions regarding Polarization Energy Calculation

lumb etc) from gromacs simutation? Thanks, Jesmin On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan 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 was u

Re: [gmx-users] Questions regarding Polarization Energy Calculation

, Aug 14, 2012 at 1:26 AM, Mark Abraham 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

[gmx-users] Questions regarding Polarization Energy Calculation

al file that does not work always :-( 5. 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

Re: [gmx-users] About getting running time from a Gromacs Run

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 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

[gmx-users] About getting running time from a Gromacs Run

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