Dear Justin,
Dear all
you guessed right.
I am now using a v-rescale thermostate
and it works fine and it also runs in parallel.
Here below the changed part in my grompp with the v-rescale thermostate.
Thanks a lot
Ivan
###
;OPTIONS FOR ANNELING
annealing
There is a AMBER FF for this kind of nitroxide spin labels. See PCCP 12
(2010) 11697.
Hope it helps,
Gerrit
Simone Cirri wrote:
Hi all,
I have a question regarding a new parameterization: actually, I'm
wondering whether or not it is possible to do it.
The molecule is tempol; you cand find
On 23/03/2011 4:42 PM, Praveen Kumar Madala wrote:
Hi,
I am new to GROMACS and I am trying to perform a MD run in PBC
condition with water as solvent.
I want to keep the crystal water molecules different from explicit
waters, I believe this helps me in analysis of crystal waters.
You can
Just an update, I decided to create a new residue for an isolated GMP. Well,
not really, because I used pdb2gmx to output a topology of a dimer, and then
modified it carefully to extract the topology of a phosphorylated GTP.
thank you !
On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic
wrote:
>
Dear Users,
I need to calculate the angular velocity correlation function. From the
gromacs discussion forum, I understand that one should be able to use
g_rotacf to calculate the angular velocity correlation function (
http://oldwww.gromacs.org/pipermail/gmx-users/2004-September/012278.html).
Ho
Hello users,
Although there was already much discussion had been done on the procedure to
construct DCCM map from covar.dat(i.e. output from g_covar) but still I am
not clear
with the step wise procedure to calculate the correlation matrix from
covarience matrix(covar.dat).
1) It is stated in the
Hi Justin,
On 3/22/11 6:57 PM, Justin A. Lemkul wrote:
1. manual.gromacs.org no longer has any useful content. The site
comes up with "syrah.cbr.su.se" and nothing else. Are there changes
going on with this site?
I moved the manual to the new server and now it's accessible again.
Cheers,
R
Dear Justin
I download the script "plot_hbmap.pl" and input "perl $0 -s b4md.pdb -map
hbmap.xpm -index hbond.ndx\n",
but the output info is "Unrecognized switch: -bash (-h will show valid
options).";
then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index
hbond.ndx\n"
Dear gmx-users,
I'm experimenting a LINCS warning on my system, an enzyme with ATP,
galactose and Mg. We started from the crystallographic structure, made some
accommodation on the topology of the sugar in order to check for partial
charges (according to Justin Lemkul's suggestions on PRODRG server
Dear Justin
I download the script "plot_hbmap.pl" and input "perl $0 -s b4md.pdb -map
hbmap.xpm -index hbond.ndx\n",
but the output info is "Unrecognized switch: -bash (-h will show valid
options).";
then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index
hbond
On 23/03/2011 9:45 PM, Anna Marabotti wrote:
Dear gmx-users,
I'm experimenting a LINCS warning on my system, an enzyme with ATP,
galactose and Mg. We started from the crystallographic structure, made
some accommodation on the topology of the sugar in order to check for
partial charges (accordi
On 23/03/2011 3:39 PM, Elisabeth wrote:
Thanks Mark for the hints. I am using a pre equilibrated box for both
runs. Can you again explain how Can I interpret this from fluctuations
from two runs? Below is the resutls from two versions: Thanks!
IIRC the contents of the .edr file didn't change a
Mark Abraham wrote:
On 23/03/2011 3:39 PM, Elisabeth wrote:
Thanks Mark for the hints. I am using a pre equilibrated box for both
runs. Can you again explain how Can I interpret this from fluctuations
from two runs? Below is the resutls from two versions: Thanks!
IIRC the contents of the
gromacs564 wrote:
Dear Justin
I download the script "plot_hbmap.pl" and input "perl $0 -s
b4md.pdb -map hbmap.xpm -index hbond.ndx\n",
but the output info is "Unrecognized switch: -bash (-h will show valid
options).";
then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.
Thanks for your help. :)
On 23 March 2011 07:47, Justin A. Lemkul wrote:
>
>
> Mark Abraham wrote:
>
>> On 23/03/2011 3:39 PM, Elisabeth wrote:
>>
>>> Thanks Mark for the hints. I am using a pre equilibrated box for both
>>> runs. Can you again explain how Can I interpret this from fluctuations
Hello,
I have a little problem with FE output file. Below is the settings and also
I am including -dgdl in the command I issue but no dgdl (or dhdl) file
generates. I dont figure where the problem lies ! (version 4.5.3).
free_energy = yes
init_lambda = 0
delta_lambda
Moeed wrote:
Hello,
I have a little problem with FE output file. Below is the settings and
also I am including -dgdl in the command I issue but no dgdl (or dhdl)
file generates. I dont figure where the problem lies ! (version 4.5.3).
How long has the simulation been running? Output is b
Hi Chris,
I experienced the same kind of thing. In the process of building a box
of liquid (organic solvent), at some point I wanted to get rid of a
layer of vacuum around my system. So for shrinking the box I used
similar settings as you and found also that the collapse was going
slower than
Hi Chris,
recently one of my students made a mistake during the model system assembling,
setting the initial volume to a value three times larger than expected
by the density.
after 1 microsecond (coarse grained MD, of course) there were droplets
and vacuum
between them, and the volume did not sh
> Hi Justin,
>>
>
I was looking all the time for a file with dgdl extension throughout the
directory. IIRC in previous versions -dgdl would generate such extension. I
found now .xvg file which has dhdl data. (if I am right dgdl is the very
dhdl in 4.5.3!)
> I have a little problem with FE output
Thanks Patrick and Andre!
We repeated this with a few box sizes just to get a quick handle on
it. The equilibrium volume is about 64 nm^3. If we start with a volume
of 1000 nm^3 then the overall box does not collapse at all within 200
ps of NPT Langevin dynamics at 1 atm.If we start with a
ahmet yıldırım wrote:
Dear Justin,
You said "You didn't properly account for PBC. Watch the trajectory -
you should see distinct jumps across the box." for attached figure.
What should I do?
Exactly as I said. Watch the trajectory to see if my guess is right. If the
molecule is danci
Moeed wrote:
Hi Justin,
I was looking all the time for a file with dgdl extension throughout the
directory. IIRC in previous versions -dgdl would generate such
extension. I found now .xvg file which has dhdl data. (if I am right
dgdl is the very dhdl in 4.5.3!)
The extension h
Hi,
Your foreign_lambda value is only one, please put all your lambda values
separated by space and you will get the dhdl file. And make sure that
you use -deffnm when you run your mdrun to get all the out put files by
default.
Cheers,
From: gmx-users-boun...@gromacs.org
[mailto:gmx-use
Emanuel Birru wrote:
Hi,
Your foreign_lambda value is only one, please put all your lambda values
separated by space and you will get the dhdl file. And make sure that
This is not required. You can specify as many or as few foreign_lambda values
as you like.
you use –deffnm when you
Hi Justin,
Sure what you wrote is correct, what I am trying to tell to him is that
if he has more than one foreign lambda it is better to put all of them
as it is not logical to use only one foreign lambda to calculate FE (0 -
0.1) and he doesn't have delta lambda too. -Deffnm is sure all about
fi
Emanuel Birru wrote:
Hi Justin,
Sure what you wrote is correct, what I am trying to tell to him is that
if he has more than one foreign lambda it is better to put all of them
as it is not logical to use only one foreign lambda to calculate FE (0 -
0.1) and he doesn't have delta lambda too. -De
Hello everybody,
I want to use the no cut-off option in gromacs for the electrostatic
interactions. In manual it says for this I need to define: pbc=no;
nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file.
My questions are:
1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a
Hi Justin,
It good that the issue is solved. As per my experience if you want to do
a series of simulations it is not necessary to use foreign_lambda, for
each simulation we can give different lambda values starting from 0 to
1( from fully interactive to non-interactive) no need of foreign_lamda
a
Emanuel Birru wrote:
Hi Justin,
It good that the issue is solved. As per my experience if you want to do
a series of simulations it is not necessary to use foreign_lambda, for
each simulation we can give different lambda values starting from 0 to
1( from fully interactive to non-interactive) n
Yeah, I am using IT and do analyse the result using another method not
bar. But I used g_bar when I was using the foreign_lambda and simulate
all in a single file. I have already sent my suspect few weeks back.
I am a bit confused on the g_bar part, when it says -f expects multiple
dhdl files. Do
Hi Swarnendu,
grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should
stick to it.
Cheers,
Itamar
On 24/03/11 1:13 PM, Swarnendu Tripathi wrote:
Hello everybody,
I want to use the no cut-off option in gromacs for the electrostatic
interactions. In manual it says for this I nee
Emanuel Birru wrote:
Yeah, I am using IT and do analyse the result using another method not
bar. But I used g_bar when I was using the foreign_lambda and simulate
all in a single file. I have already sent my suspect few weeks back.
Is there an active redmine issue? I cannot find any post f
I have tried the free energy calculation using 4.5.3, but when I run
g_bar it still gives me the following and do not generate the output
files.
prod.xvg: 0.0 - 5000.0; lambda = 0.000
foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001
pts) 0.030 (125001 pts) 0.050 (125001 pts
Emanuel Birru wrote:
I have tried the free energy calculation using 4.5.3, but when I run
g_bar it still gives me the following and do not generate the output
files.
prod.xvg: 0.0 - 5000.0; lambda = 0.000
foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001
pts) 0.030 (1250
Thanks Justin,
I will revise my mdp file again and will give it a try once more. Can
you give me an idea on the following too.
I want to perform free energy calculation by changing the gd (dihedral
parameters) to fourier dihedral parameters for small molecules
(solutes). But I am getting th
Emanuel Birru wrote:
Thanks Justin,
I will revise my mdp file again and will give it a try once more. Can
you give me an idea on the following too.
I want to perform free energy calculation by changing the gd (dihedral
parameters) to fourier dihedral parameters for small molecules
(
On 24/03/2011 1:34 PM, Itamar Kass wrote:
Hi Swarnendu,
grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should
stick to it.
Cheers,
Itamar
On 24/03/11 1:13 PM, Swarnendu Tripathi wrote:
Hello everybody,
I want to use the no cut-off option in gromacs for the electrostatic
int
Hi all,
Thank you for the reply. The answer I got for the second question about
table-extension, I understand and agree with that.
Regarding my first question I asked, I did not get any error with grompp
even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I used the no
cut-off conditions wh
On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote:
Hi all,
Thank you for the reply. The answer I got for the second question
about table-extension, I understand and agree with that.
Regarding my first question I asked, I did not get any error with
grompp even when I tried rlist=rvdw=2.0 and rc
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