Dear forum users,
I am new to MD and looking for help and a little tutorial how to create a
.gro/.pdb file and calculate atom charges for a molecule I can not find
online. I have assembled the molecule's .itp file and I seek help how to
calculate charges with OPLS.
molecule: 4-Methoxyphenyl
got you. Thanks again!
Santo
-
K. P. Santo
Post doctoral fellow
Department of Chemistry
University of North Carolina at Chapel Hill
Chapel Hill, NC, USA
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013308.html
Sent from the
Hi,
Here you go!
http://pubs.acs.org/doi/abs/10.1021/jp003919d
On Fri, Dec 13, 2013 at 8:42 PM, pp0ta187 p...@live.com wrote:
Thank you Justin for a quick response.
Although, I can not find the spoken reference in the manual, could you
please point in which version is it?
--
View this
Thanks Justin.
I already added the description in the ffbonded.itp, but nothing is shown in
the topol file. I am not sure to put atom names (e.g. C9 C10) or atom type (C
C)? However, I tried both and non of them worked. I don't know what I am doing
wrong and I appreciate if you could help
On 13.12.2013 18:01, chem grad wrote:
Thank you so much!
Gromacs seems to be installed properly now.
but mdrun doesn't work, right?
M.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post?
On 13.12.2013 21:38, chem grad wrote:
I cannot convince cygwin to source the gromacs files properly (well, at least I think that's the
problem). When I enter luck into the command line it returns the luck: command
not found error message.
Also, both commands I have entered (pdb2gmx and mdrun)
On Sat, Dec 14, 2013 at 10:52 AM, Keerthana S.P Periasamy
keerthanas...@yahoo.com wrote:
On Saturday, December 14, 2013 10:51 AM, Keerthana S.P Periasamy
keerthanas...@yahoo.com wrote:
Hai
initially I used 4processors for mdrun and due to some power
fluctuations i have
