Re: [gmx-users] MDsimulation of Protein-DNA complex

[terrencesun]

Hi,

What you have described is no physical. You should avoid doing that unless you 
have a better reason. In normal MD, counter ions don't need special treatment 
such as restraint to some solute.

Regards
Terry


> On 3 May 2016, at 9:51 PM, soumi  wrote:
> 
> Dear 
> All, 
> I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN 
> force field with gromacs.In order to neutralize the net charge on the 
> protein-DNA complex by adding the correct number of positive ions or 
> negative ions I have used the following command in gromacs 
> gmx genion -s ions.tpr -o  solv_ions.gro -p topol.top -pname NA -nname CL -np 
> 38
> When prompted, I choose group 13 SOL for embedding ions because I 
> do not want to replace parts of protein-DNA complex with ions.In MM 
> optimisation process for solvated complex,counter ions are easily separated 
> from the solute .Such separated ions have no function as a counter ion.In 
> order to avoid such situation I desire the positions of Na+ ions around DNA 
> to be constrained within 5 A from the PO4- groups of DNA backbone,while the 
> Na+ ions around protein were contrained within 6 A from the carbon atom 
> of the carboxyl group of the negatively charged Asp 129 residue.How can the 
> positions of Na+ ions around DNA be constrained within 5 A from the PO4- 
> groups of DNA backbone by which command or method using gromacs 
> exclusively (not AMBER TOOL /AMBER PACKAGE )?With Regards ,Soumi Das
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[terrencesun]

Hi, 

Try gmx_mpi.

Regards
Terry


> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>  wrote:
> 
> Dear all user
> 
> I install gromacs in my laptop its perfectly ok. But i have problem to
> install in my desktop there i face problem.
> In my desktop i want to compile with cuda accelerator and MPI option. I
> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
> this driver is ok.
> 
> For gromacs i run this installation command.
> 
> tar -xzvf gromacs-5.1.2.tar.gz
> cd gromacs-5.1.2.tar.gz
> mkdir build
> cd build
> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
> make -j16
> make check
> sudo make install -j16
> 
> source /usr/local/gromacs/bin/GMXRC
> 
> In the installation procedure i dont find any error. All 26 test completed
> without error.
> 
> But when i try to run "gmx or gmx help"
> 
> There is error no command gmx found. I need your guidance.
> 
> Best Regards
> 
> -- 
> *Md Imrul Reza Shishir*
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Re: [gmx-users] multi threads pinning problem

[terrencesun]

Hi,

The -pin is used to prevent the OS switching threads across physical cores, 
which may result in performance loss. If you want to pin your threads to cores, 
use -pin on. -pinoffset can help you set to which cores your threads are 
pinned, which is stated in mdrun -h.

Regards
Terry


 On 24 Jul 2015, at 11:53 am, Zhenyu Meng fdmm1...@gmail.com wrote:
 
 Dear all,
 When I'm running gromacs with mdrun, I always receive such message:
 
 The number of threads is not equal to the number of (logical) cores
 and the -pin option is set to auto: will not pin thread to cores.
 This can lead to significant performance degradation.
 Consider using -pin on (and -pinoffset in case you run multiple jobs).
 
 The server I use has 128 cores, and usually I use mdrun with flag -nt 32 or
 -nt 64 to specify the threads, I also notice there's large performance lost
 in each run.
 I wonder what's the difference between '-pin on' and '-pinoffset'. I
 usually run multi jobs on the server so will '-pin on' or '-pinoffset'
 affect the other jobs? If I use '-pinoffset' what value I should
 set(suppose I have already use 32 cores for other jobs)?
 
 -- 
 Sincerely,
 Mr. Meng Zhenyu
 Division of Chemistry and Biological Chemistry
 School of Physical and Mathematical Sciences
 Nanyang Technological University
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