[Fwd: Re: [gmx-users] VSMP cluster performance changes with time]

-- similar for next steps. regards anupam > On 18/08/11, Anupam Nath Jha wrote: > >> >> >> Dear all >> >> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes. >> >> I am writin

Re: [gmx-users] VSMP cluster performance changes with time

-- similar for next steps. regards anupam > On 18/08/11, Anupam Nath Jha wrote: > >> >> >> Dear all >> >> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes. >> >> I am writin

[gmx-users] VSMP cluster performance changes with time

Dear all I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes. I am writing log files for different ns (1-10) in different files i.e. different files for each nano second . The performance goes like following: -- for 1st ns: (Mnbf/s) (GFlops

Re: [gmx-users] numerical matrix from xpm file

ict([col(xpm.readline()) for i in range(nc)]) > > for i in xpm: > if i.startswith("/*"): > continue > j = unquote(i) > z = [colors[j[k:k+nb]] for k in range(0,nx,nb)] > sys.stdout.write(" ".join(z)+"\n") > > ### > > On Mo

Re: [gmx-users] numerical matrix from xpm file

> No, there's no ability to do this. I think there should be, though, and seem > to > recall discussion of it on one or other mailing list or the web page. > > Mark > > - Original Message ----- > From: Anupam Nath Jha > Date: Saturday, October 2, 2010 21:32

[gmx-users] numerical matrix from xpm file

Hi all Is it possible to obtain the matrix in numeric form from xpm (obtained from gromacs analysis) files. because it's not coming in options for ourput files. thanks with regards anupam -- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed

Re: [gmx-users] rmsd between different monomers

/2010 9:29 PM, Justin A. Lemkul wrote: >> >> >> Anupam Nath Jha wrote: >>>> >>>> Anupam Nath Jha wrote: >>>>> Dear all >>>>> >>>>> I made an index file with 4 different groups for 4 different chains >>>&g

Re: [gmx-users] rmsd between different monomers

> > > Anupam Nath Jha wrote: >> Dear all >> >> I made an index file with 4 different groups for 4 different chains (since my >> protein is a tetramer) and then run >> >> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out >> >> to

[gmx-users] rmsd between different monomers

t;C-alpha_chain2 after lsq fit to C-alpha_chain1" 0.0000.001 so the rmsd = 0.001 whereas when I use online server it gives me 1.4. so what am I doing wrong? regrads anupam -- Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Ban

[gmx-users] rmsd between different monomers

ce is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-229

[gmx-users] not running on higher no of nodes

lection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

[gmx-users] scalability of gromacs-3.3

cts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanne

Re: [gmx-users] karthik

)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a

[gmx-users] gromacs installation in IBM BLUEGENE

in advance anupam -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara La

Re: [gmx-users] angle between helices

HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam > Marc F. Lensink wrote: >> On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: >>> Anupam Nath Jha wrote: >>>> Dea

[gmx-users] angle between helices

Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users

[gmx-users] is there any size limit for simulation in gromacs

stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and

Re: [gmx-users] installation

f stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily sciece. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-

Re: [gmx-users] lipid simulations

hi thanks for such a brief reply.. i have already downloaded these four files from the Peter Tieleman's website: "dppc128.pdb dppc.itp inflategro.pl lipid.itp" but it looks like it has been simulated in water box for some time.. am i right? (i am afraid that i will not) then what's next and wh

[gmx-users] lipid simulations

Dear all i want to know about lipid molecule (as dppc) simulations. i am new in gromacs, i have used it for globular proteins but i am not very clear in case of membrane proteins. i have gone through literature and know the steps but not the technical details. as like what parameters should I use

Re: [gmx-users] how to run parallel jobs in gromacs

num=2 numhosts=1 there are not enough hosts on which to start all processes > Anupam Nath Jha wrote: >> Dear all >> >> i am new in gromacs. i have installed gromacs-3.3.3 in our cluster(mpi is >> already there) with parallel version (using the following command): &g

Re: [gmx-users] how to run parallel jobs in gromacs

hy it is trying to start 3 processes... > > Cheers, > > Erik > > On Aug 6, 2007, at 12:46 PM, Anupam Nath Jha wrote: > >> Dear all >> >> i am new in gromacs. i have installed gromacs-3.3.3 in our cluster >> (mpi is >> already there) with p

[gmx-users] how to run parallel jobs in gromacs

ks in adavnce anupam -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily sciece. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560