Re: [gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial

On 5/20/13 9:00 AM, Vishal Kumar Jaiswal wrote: LAPTOP- WORKING PC -NOT WORKING Gromacs version:VERSION 4.6.1 VERSION 4.6.1 Precision: single

Re: [gmx-users] compile Gromacs using Cray compilers

Hi, I agree with Mark that it is probably not worth it. Why are you interested in it? Are you working on the Cray compiler or planning to use some specific features? You need to apply the patch here: https://gerrit.gromacs.org/#/c/2343/ to get it to compile. But of course then it will still be mu

Re: [gmx-users] compile Gromacs using Cray compilers

Hi, Fixing or working around Cray's compilers (whether atomic support or vector intrinsics) is really not worth any of our time if gcc+mpi is available. Mark On Tue, May 21, 2013 at 12:40 AM, Humayun Arafat wrote: > Hi Roland, > > I can actually try to solve some issues with Cray compiler if

Re: [gmx-users] compile Gromacs using Cray compilers

Hi Roland, I can actually try to solve some issues with Cray compiler if you can give me some idea what is needed. Currently I get error for the atomic.h inside thread_mpi. I think it needs intrinsics. Maybe there are some others as well. Please let me know the issues. thanks On Mon, May 20,

Re: [gmx-users] compile Gromacs using Cray compilers

On Mon, May 20, 2013 at 1:23 PM, Humayun Arafat wrote: > I am only interested in GPU code. > Is there anyway I can just run this using cray compilers? Why do you want to use the cray compilers? As Mark said those aren't supported. We reported the problems with them to Cray but AFAIK they haven't f

Re: [gmx-users] Re: QM/MM simulations

On 5/20/13 10:19 AM, DavidPO wrote: I send you "output.txt". These is the information that the program produces in terminal I also send you the "CMakeCache.txt" file as you request. Please check them out. David CMakeCache.txt ou

Re: [gmx-users] How to visualize .gro file without .tpr file

Alternatively, you can use editconf -f (tpr file) -o (pdb file) to convert .gro to .pdb, and then use the visualization tools such as Pymol to view it. On Tue, May 21, 2013 at 1:01 AM, Vishal Kumar Jaiswal wrote: > Vmd can visualise a GRO file directly without .tpr . I use it to visualise > gro

Re: [gmx-users] How to visualize .gro file without .tpr file

Vmd can visualise a GRO file directly without .tpr . I use it to visualise gro files On Tue, May 21, 2013 at 12:59 AM, Bao Kai wrote: > HI, all, > > I have a small question here. I usually use ngmx to visualize the > .gro or .trr file with a .tpr file. > > While after simulation, I use editco

[gmx-users] How to visualize .gro file without .tpr file

HI, all, I have a small question here. I usually use ngmx to visualize the .gro or .trr file with a .tpr file. While after simulation, I use editconf to generate a new .gro file. Then I failed to visualize the new .gro file since the .tpr file did not work for the new .gro file now. I wonder if

Re: [gmx-users] compile Gromacs using Cray compilers

I am only interested in GPU code. Is there anyway I can just run this using cray compilers? thanks On Mon, May 20, 2013 at 12:06 PM, Szilárd Páll wrote: > The thread-MPI library provides the thread affinity setting > functionality to mdrun, hence certain parts of it will always be > compiled in

Re: [gmx-users] compile Gromacs using Cray compilers

The thread-MPI library provides the thread affinity setting functionality to mdrun, hence certain parts of it will always be compiled in, even with GMX_MPI=ON. Apparently, the Cray compiler does not like some of the thread-MPI headers. Feel free to file a bug report on redmine.gromacs.org, but *don

Re: [gmx-users] compile Gromacs using Cray compilers

Hi, I enabled mpich2 and used that to compile gromacs using this command cmake -DGMX_MPI=ON .. But I am still getting the error. [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_thread_affinity.c.o CC-20 craycc: ERROR File = /home/users/mmm/gromacs/include/thread_mpi/atomic.h, Line =

Re: [gmx-users] About Production MD run error

On 5/20/13 11:42 AM, vidhya sankar wrote: Dear Justin Thank you for previous reply. I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by

[gmx-users] About Production MD run error

Dear Justin Thank you for previous reply.   I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide) After Successful  NPT and NVT

Re: [gmx-users] compile Gromacs using Cray compilers

Specify an MPI compiler and use cmake -DGMX_MPI=on by itself. That is mutually exclusive with thread mpi. Mark On Mon, May 20, 2013 at 5:01 PM, Humayun Arafat wrote: > Hi, > > I tried different options. > > cmake -DGMX_MPI=ON/OFF .. > cmake -DGMX_THREAD_MPI=OFF/ON .. > > I tried both of these

Re: [gmx-users] compile Gromacs using Cray compilers

Hi, I tried different options. cmake -DGMX_MPI=ON/OFF .. cmake -DGMX_THREAD_MPI=OFF/ON .. I tried both of these two flags together. But none of them worked. The compilation fail in either gmx_omp.c or gmx_thread_affinity.c Can you please suggest me another way to turn off the thread mpi? Thank

[gmx-users] Re: QM/MM simulations

I send you "output.txt". These is the information that the program produces in terminal I also send you the "CMakeCache.txt" file as you request. Please check them out. David CMakeCache.txt output.txt

Re: [gmx-users] About CNT cyclic PEptide

On 5/20/13 9:30 AM, vidhya sankar wrote: Dear Mark/justin Thank you for Previous reply My Final Production MD only shows Error Like Lincs , System Exploding And segmentation Fault TO Avoid this May I Further Extend My equilibration from 2 ns to 10 ns ? Gi

[gmx-users] About CNT cyclic PEptide

Dear Mark/justin Thank you for Previous reply My Final Production MD only shows Error Like Lincs , System Exploding  And segmentation Fault TO Avoid this May I Further Extend My equilibration from 2 ns to 10 ns ? Thanks in Advance -- gmx-users mailing list

[gmx-users] Re: QM/MM simulations

I send you "output.txt". These is the information that the program produces in terminal I also send you the "CMakeCache.txt" file as you request. CMakeCache.txt output.txt

Re: [gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial

LAPTOP- WORKING PC -NOT WORKING Gromacs version:VERSION 4.6.1 VERSION 4.6.1 Precision: single same Memory model: 32 bit

Re: [gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial

On 5/20/13 2:29 AM, Vishal Kumar Jaiswal wrote: I am trying to complete the lysozyme in water tutorial in gromacs 4.6.1 and i am getting this error in the energy minimization step I was able to complete the entire tutorial on another computer ( my personal laptop) . ( I was getting the same err

Re: [gmx-users] residues interaction with ligand

You can use g_select utility. For more details check the following link http://www.gromacs.org/Documentation/Gromacs_Utilities/g_select On Sun, May 19, 2013 at 1:20 PM, Arunima Shilpi wrote: > Respected Sir > > If we have to find the residues surrounding the ligand in protein ligand > complex...

Re: [gmx-users] About CNT wrapped by Cyclic peptide

On Mon, May 20, 2013 at 12:25 PM, vidhya sankar wrote: > Dear Mark and Justin Thank you for yours previous Replies; > You Mailed ME that My NVT and NPT equilibration is seems to be crashed . > But Actually My NVT Equlibration and NPT Equlibation was Sucessfull It > gives Nice output without

[gmx-users] About CNT wrapped by Cyclic peptide

Dear Mark and Justin  Thank you for yours previous  Replies; You Mailed ME that My NVT and NPT  equilibration is seems to be  crashed . But   Actually My NVT Equlibration and NPT Equlibation was Sucessfull It  gives Nice output  without Lincs  warning ,  System exploding  But My Question Is there

Re: [gmx-users] RNA MD Simulation using GROMACS

Hi, To get useful help with this issue you need to provide a more informative description of what when wrong, i.e. what gromacs tool was invoked and what input was used. Erik On 20 May 2013, at 10:59, Pruthvi Bejugam wrote: > Hi all, > >I want to perform a RNA (Just RNA no p

[gmx-users] RNA MD Simulation using GROMACS

Hi all, I want to perform a RNA (Just RNA no protein or DNA included) MD Simulation. Can anybody suggest me what are the general parameters should be used for the RNA MD Simulations. I know that AMBER and CHARMM force field work well for DNA and RNA. i have tried the RNA MD simulat

Re: [gmx-users] Re: DD fails

Looks ugly :-( Can you reproduce it? With 4.5.7? Mark On Mon, May 20, 2013 at 7:43 AM, Dr. Vitaly Chaban wrote: > UPD: the version of gromacs exhibiting this marvellous behavior is 4.5.5. > > > > On Mon, May 20, 2013 at 8:11 AM, Dr. Vitaly Chaban >wrote: > > > any ideas what the below error me

Re: Re: [gmx-users] Expanding a .top file to have all connection information

On Mon, May 20, 2013 at 4:36 AM, David Rosenman wrote: > Hello again, > > Sorry for the delay in my response. > > The original top file is: > http://wikisend.com/download/951610/APPTM_WT.top > > The grompp -pp processed top is: > http://wikisend.com/download/851584/APPTM_WT_processed.top > > > The