mpirun -np" and
"mdrun_mpi -nt" etc...
Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For
t; etc and nothing seems to help...
What is my problem???
Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe
n would be
extremely helpful!!! Thanks Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://mail
I got the following errors when I tried to install gromacs MPI version 5.0.4 on
a Fedora 18
I wrote on the command line the following:
cmake '/home/steve/Downloads/gromacs-5.0.4'-DGMX_BUILD_FFTW=ON -DGMX_MPI=ON
SCREEN PRINT OUT: -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so --
Thanks for your response. I have attached the files you asked forThe
"Cmake_Screen.output" contains, at start, my cmake input command....
-Steve
On 9/20/16 2:52 PM, Steve Seibold wrote:
> Hello
> I am attempting to compile Gromacs 5.0.4 mpi version and I get the state
3f.so. The libfftw3f.so
is a symbolic link to libfftw3f.so.3.2.4..Not sure what is going on
In addition, I could not locate the GMXR executable for gmx??
Can someone help me with this???
Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.o
? Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/lis
where in the screenprint outs or the
gro files or system.top files… I also made sure that I was not getting a “cpp”
error…. Does anyone know what the problem is here??? Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
install 5.1.x but it
failed...If necessary I will attempt to install 5.1.x, but only if it is
necessary
thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromac
the grompp to make a tpr file.I have also place
in "disre_fc = 1000" in my mdp file
Can someone be explicit about what I am doing wrong...I did get the "position
restraint" to work, but am having trouble here.
Thanks, Steve
--
Gromacs Users mailing list
I apologize if this is a really crazy question; I just want to be sure that I
understand everything.
I am assuming after reading the Replica Exchange from the on-line gromacs site
that you cannot run, perform this method with multiple threads on one one
system. You must have several machines wi
I am doing a simulation of a protein with zinc ligands..When looking
calculating the distance between the Zinc and the water, I am getting distances
that go as low as 0.3-0.4 Angstroms. This seems too close to me..Is this close
contact due to the errors in trajectories??
Thanks, Steve
it showed that this worked, but only for
ONE zinc ligand ion...the other left the box with ligand to sulfur bond on
30-40 angstroms.
Can someone tell me what is going on here...???
Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Suppo
(positions) back onto initial structure which is in center of
box.
trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit
progressive -o protein13A.trr
This didn't help at all..
I am really at a loss here on how to deal with this and could use some help..
Steve
--
or if I use the whole
protein...It is only when I attempt to get the rms of the C-terminus region
that I get this graphing problem (traj plots look like Histograms)Not sure
what this means since if I observe
the trajectories in VMD the whole protein breaks up
Thanks, Steve
--
Gromacs Use
procedure:
trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc
However, this did not correct the problem...Can someone please inform as to
what the problem is??? The total energy and potential energy looks ok and so, I
am lost as to what is happening or how to fix it.
Thanks, Steve
--
Gromacs
est in a
small Linux cluster (~ 20-30 nodes) than to assemble this Apple cluster?
Thanks, Steve
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Apple-cluster-tp5014900.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Gromacs Users mailing list
Thanks Justin I appreciate you help...Your comments made it clear...
Steve
--
View this message in context:
http://gromacs.5086.x6.nabble.com/problems-with-Cysteines-tp5013859p5013870.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Gromacs Users mailing list
not
allow any changes to Cys (to make s-s bonds or anything). Am I doing
something wrong here?
Could someone please tell me what I can do to make a S-S bond...do I have to
use "specbond.dat"???
Thanks, Steve
--
View this message in context:
http://gromacs.5086.x6.nabble.com/pro
Hello
I am trying to make CYS in my topology file (and NOT CYSH or dissulfide
bond). If my pdb file calls for Cys, I get CYSH .rtp type.
I Then attempted to test the -ss command using pdb2gmx and this command is
completely ignored. I don't get an error or any output suggesting its usage.
I am us
older than 2.0
Make a new one with grompp or use a gro or pdb file, if
possible
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Thanks, Steve
--
View this message in context:
http://gromacs.5086.x6
ine incorrectly. Here is
what I have:
$editconf -f name.pdb -o name2.pdb -conect
I have a topology file in my working directory.
I searched on line and in the forum, but can't find any info. Did I miss it?
I would really appreciate any help.
Thanks, Steve
--
View this message in cont
"Unknown residue: %s\n"%resn
ValueError: Unknown residue: ALA
Therefore, I must have my "Mapping" directory in the wrong location?? I
placed it in both the working directory and in /home/stevesei/bin but I keep
getting the above message.
I would appreciate any help..tha
Martini FF?
Thanks, Steve
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/ma
24 matches
Mail list logo