On 06/24/2011 02:21 PM, Makoto Yoneya wrote:
Dear GROMACS experts:
I'd tried to use a GBSA implicit solvent function in ver. 4.5.4.
I'd convinced the normal run with vacuo with simply high epsilon_r
setting.
After that, I'd modified the topology stuff by adding
[ implicit_genborn_params ]
entry
Dear users,
Any suggestions?
Thank you
M. Kavyashree
On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
In one of the simulations while calculating box dimensions
using g_energy this output was obtained -
Statistics over 5001 steps [ 0. through
Hello! I have a misunderstood about the installation of gpu-enabled
gromacs under windows.
I'll try to explain: in system requirements of gromacs-gpu it is wrote
that Nvidia CUDA libraries have to be installed. But is it possible to
do under cygwin? This quertion appears because we run gromacs
Hi all
I have set up a simulation with PBC using PME and specify an energy
group enclusion involving some virtual sites and a hydrocarbon chain.
i.e. hydrocarbon chain is one energy group and the virtual sites
constitute the other group. Grompp generates the following warning
Can not exclude the
Kavyashree M wrote:
Dear users,
Any suggestions?
You haven't provided nearly enough diagnostic information for anyone to offer
you any useful help (as Mark said yesterday). For example, please provide:
1. Your exact g_energy command line
2. The output of gmxcheck for this .edr file
3.
Gavin Melaugh wrote:
Hi all
I have set up a simulation with PBC using PME and specify an energy
group enclusion involving some virtual sites and a hydrocarbon chain.
i.e. hydrocarbon chain is one energy group and the virtual sites
constitute the other group. Grompp generates the following
Kavyashree M wrote:
Sir,
I am sorry I did not get any mail for that query since I posted it.
So I had to ask once again..
1. g_energy -f ener.edr -o box.xvg
selecting 15 16 17 0
2. gmxcheck -e ener.edr
Opened ener.edr as single precision energy file
frame: 0 (index 0),
Sir,
I am sorry I did not get any mail for that query since I posted it.
So I had to ask once again..
1. g_energy -f ener.edr -o box.xvg
selecting 15 16 17 0
2. gmxcheck -e ener.edr
Opened ener.edr as single precision energy file
frame: 0 (index 0), t: 0.000
Last
Hi Justin
Thanks for the reply. I take it then, if I use the maxwarn option, it
will still apply the exclusion for the short-range non-bonding interactions.
Cheers
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
I have set up a simulation with PBC using PME and specify an energy
Gavin Melaugh wrote:
Hi Justin
Thanks for the reply. I take it then, if I use the maxwarn option, it
will still apply the exclusion for the short-range non-bonding interactions.
Yes, that should work. The error message is only there to prevent people from
erroneously thinking they can
Sir,
I tried it already but It was huge file. this kind of nan comes only
for RMSD not for any other term. I will try looking into that file again.
Thanks
With regards
M. Kavyashree
On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
I am
Kavyashree M wrote:
Sir,
I tried it already but It was huge file. this kind of nan comes only
for RMSD not for any other term. I will try looking into that file again.
Let's keep on topic and focus on the box vectors; changing the subject midway
makes it harder to arrive at a solution.
Sir,
I went through the whole .edr file for one
specific term in which I was getting nan.
Of the three columns (Energy; Av. Energy; Sum Energy)
order (power) for temperature did not change at all in the
first column but in the second column there was a change of
power between +1 and +2 which was
Kavyashree M wrote:
Sir,
I went through the whole .edr file for one
specific term in which I was getting nan.
Of the three columns (Energy; Av. Energy; Sum Energy)
order (power) for temperature did not change at all in the
first column but in the second column there was a change of
power
Sir,
Thats right. But what I felt was, all these
problems are connected. (I dont mean that
temperature is connected to box dimension)
Actually I was getting nan under RMSD for all
the energy terms.
I have checked the total energy graph also it
is stable.
even in case of box dimentions I checked
Sir.
I am sorry for changing the topic. It was not intentional
It just came as I wanted to mention the other part of the
problem that data had.
I have checked the entire file of the gmxdump output
of ener.edr firl for Box dimention as well as Temp.
Thanks
With Regards
M. Kavyashree
On Fri, Jun
Kavyashree M wrote:
Sir.
I am sorry for changing the topic. It was not intentional
It just came as I wanted to mention the other part of the
problem that data had.
I'm trying to focus the discussion because you've presented three separate
(maybe related) issues:
1. Wrong number of
Hello,
I have some doubts regarding the output file correl.dat as it contains 3
columns, but I am not able to get what are
these column contains,I mean how to change it to the format in which I can
directly plot the data to get DCCM map...
For e.g in this form
Res1 Res2 Correlation coefficient
x
Hello,
I just want to ask that in g_dist module, -dist option expect distance as a
real argument, so the distance should be in nm or A for that...
--
---
*Regards,*
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
bipin singh wrote:
Hello,
I just want to ask that in g_dist module, -dist option expect distance
as a real argument, so the distance should be in nm or A for that...
Please read the manual, Chapter 2.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
On Fri, Jun 24, 2011 at 10:45 AM, bipin singh bipinel...@gmail.com wrote:
Hello,
I just want to ask that in g_dist module, -dist option expect distance as a
real argument, so the distance should be in nm or A for that...
-nanometer (nm)
--
---
*Regards,*
Bipin Singh
Dear Adam:
I have a number of questions listed below. But first, I think it would
be useful if you explain exactly what you want to accomplish and how
you tried to do this with non-modified code and what problem you ran
into that caused you to modify the code. After you outline that,
Thanks...
On Fri, Jun 24, 2011 at 20:17, shivangi nangia shivangi.nan...@gmail.comwrote:
On Fri, Jun 24, 2011 at 10:45 AM, bipin singh bipinel...@gmail.comwrote:
Hello,
I just want to ask that in g_dist module, -dist option expect distance as
a real argument, so the distance should be in
Hi Bipin,
Read them in as a vector of numbers and divide them into sqrt(len(vector))
rows to get yourself a nice square correlation matrix.
Cheers,
Tsjerk
On Jun 24, 2011 3:28 PM, bipin singh bipinel...@gmail.com wrote:
Hello,
I have some doubts regarding the output file correl.dat as it
Dear user,
When projection of a trajectory (50ns) on an eigen vector
was visualised in pymol, there was broken chains, but when
I projected the simulation (continued for 50 more ns ie.,
total 100ns) this broken chain was not seen why?
Thanking you
With Regards
M. Kavyashree
--
gmx-users mailing
Did you make the molecules whole and removed jumps (in case of a multimer)
prior to filtering?
Cheers,
Tsjerk
On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear user,
When projection of a trajectory (50ns) on an eigen vector
was visualised in pymol, there was broken chains,
I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr.
xtc and load it onto a pdb/gro using vmd. Then it should not be a problem.
Best Wishes,
Sarath
Did you make the molecules whole and removed jumps (in case of a multimer)
prior to filtering?
Cheers,
Tsjerk
On Jun
Dear Mark:
Thank you for your comment.
You don't say what your force field is, but those symptoms are
suggestive of a problem with CHARMM force field lacking Urey-Bradley
interaction parameters for atoms 1-2-3. If so, this is not a GB problem
per se.
Mark
Sorry for the lack of info.
Hello Sir,
It is not a multimer sir, I was a single chain protein
which was intact while submitting to MD. It has no problem
when I project the 100ns trajectory on the vector but only
in case of half of this time -50ns, it has problem.
Thank you
With Regards
M.Kavyashree
On Sat, Jun 25, 2011 at
Sir,
Yes exactly I did the same. I will try with this option now.
Thanks.
With Regards
M. Kavyashree
On Sat, Jun 25, 2011 at 2:01 AM, Sarath Chandra Dantu dsar...@gwdg.dewrote:
I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr.
xtc and load it onto a pdb/gro using
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