Hi,
yes that helps a lot. One more question. What filesystem on hopper 2 are you
using for this test (home, scratch or proj, to see if it is Lustre or GPFS)
? And are you running the test on the login node or on the compute node?
Thanks
Roland
On Wed, Jun 8, 2011 at 1:17 PM, Dimitar Pachov
Thank you for the advice Dr. Warren,
I often find the same problem with charges and parameters, and have pulled some
from the web in some instances. I have an old CRC book with tables when in
doubt,
But I wounder if anyone is interested in just making a tabulation, or wiki site
to deposite
Hi Justin
I think what is happening is that grompp is returning the projection of
the current vector between the two reference groups onto the stated
vector in the mdp file. i.e the dot product of the two vectors. The
resulting PMF plot must therefore be a function of this varying cross
product.
Thank you all for your comments! Let me give you more details about my case:
I want to study the interaction modes of known inhibitors with the monomeric
state of an IDP (~100 aa). IDPs only assume secondary structure when in
complex with their partners, hence there are no crystal structures of
Hi Igor,
Thanks for the reply but I think you slightly missed the point I was
trying to make. I followed the approach you mention for the double bond
and (with the two force fields I tried) got the values I discussed in my
last email, which when compared to the published values seem to be
hello
My feeling is that you can probably get meaningfull result by using implicit
water model plus some experimental constrain. If you have a well defined
reaction coordinate, umbrella sampling will help. As you planed, you can
also simulate unfolding process and just invert it to get the
Hi,
On Thu, Jun 9, 2011 at 2:55 AM, Roland Schulz rol...@utk.edu wrote:
Hi,
yes that helps a lot. One more question. What filesystem on hopper 2 are
you using for this test (home, scratch or proj, to see if it is Lustre or
GPFS) ?
I used home.
And are you running the test on the login
Hi,
Both the trajectories are 100 ns in length (plus I have a repeat of each
simulation using different starting velocities). The results from a
block analysis, and analysis of the repeat simulations, give almost
identical results to those in my previous message. The other thing is
that the
Hi,
A force file like this does exist
(http://pubs.acs.org/doi/abs/10.1021/jp800687p) but be aware, like the
CHARMM27 force field it is based upon, you will need to use
surface-tension to keep these lipids in the correct phase.
Cheers
Tom
Justin A. Lemkul wrote:
Ioannis Beis wrote:
Dear all ,
I want to simulate a double walled nano tube in spc water i had
made the pdb file now if i use g_x2top for creating the topology file it
gives me the following error .
Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa*
it gives the following error
*Can not find
sreelakshmi ramesh wrote:
Dear all ,
I want to simulate a double walled nano tube in spc water i
had made the pdb file now if i use g_x2top for creating the topology
file it gives me the following error .
Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa*
it gives the
I also found this usefull, but have a question on what one would consider the
standard. from eyeballing mostly the charges I get for .itp files from PRODRG
server fall into mullikin charges, but usually 3-4 dont or have no charge, but
I woundered if the ESP or AIM charges would be beter. From
lloyd riggs wrote:
I also found this usefull, but have a question on what one would consider the
standard. from eyeballing mostly the charges I get for .itp files from
PRODRG server fall into mullikin charges, but usually 3-4 dont or have no
charge, but I woundered if the ESP or AIM charges
Hi Mark,
The set of frames is arbitrary, overall I do not expect any sudden
significant change in density.
I calculated the density profiles by coinciding end of intervals, i.e
instead of 5-10, 10-15, 15-20 and 5-20 ns, I calculated 4999-1,
-15000, 14999-end and 4999 - end ps.
Dear Sir,
Thank you Sir for the clarification.
Need to explore about this.
Thanking you
With Regards
M. Kavyashree
On Wed, Jun 8, 2011 at 2:35 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
Thanks sir. I will go through them. However I have referred -
A Tutorial on Principle
Further to my last message we have managed to use a tcl script in VMD to
calculate the order parameters for the POPC chains in the CHARMM36
simulation. I have put the values for this calculation and the values I
obtained using g_order (over the same period in the same trajectory)
below (this
Dear Gromacs-users,
I compiled a single and a double precision version of gromacs 4.5.4 (MPI
enabled). The differences between single and double precision runs have been
discussed in older threads (2005/2008) in this mailing list before. At least, I
did not understand completely, which parts
On Thu, 09 Jun 2011 17:30:10 +0200
kalav...@gmx.net wrote:
Dear Gromacs-users,
I compiled a single and a double precision version of gromacs 4.5.4
(MPI enabled). The differences between single and double precision
runs have been discussed in older threads (2005/2008) in this mailing
list
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order )
yields order parameters of 0.193 and 0.051 for the first and
Dear all,
I saw an unanswered post at
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
It is about calculating local pressure in v 4.5 when using CHARMM FF. Could
someone give me some pointers about this?
Thank you
Amit
--
gmx-users mailing listgmx-users@gromacs.org
Amit Choubey wrote:
Dear all,
I saw an unanswered post at
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
It is about calculating local pressure in v 4.5 when using CHARMM FF.
Could someone give me some pointers about this?
I don't know what the development
Thanks Justin, I tried to install the recent git version but the configure
file is missing. How should I install this version ?
On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Dear all,
I saw an unanswered post at
Amit Choubey wrote:
Thanks Justin, I tried to install the recent git version but the
configure file is missing. How should I install this version ?
Run the bootstrap script. It generates the configure script.
-Justin
On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu
chris.ne...@utoronto.ca wrote:
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields
order parameters of 0.193
Dear all,
when i run energy minimization i get the following error.
the topology file was created from the starting pdb file using g_x2top
*grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3*
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
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