I do not know how to extract some special frames out (professionally),
so I just simply use vim to take the relevant models out and put into a new pdb
file.
Are there some good ways to extract one or two frames at the end of those whole
frames?
Base on your answering, now I start to suspect I mi
Dear Justin
Thank you so much for help.
I used # symbol in where you said and problem was solved. a output was
obtained with name summary_HBmap.dat.
this file is as follows:
#DonorAcceptor% Exist.
Resolved:
I have found the error. Apparently I was using -dt 20, and the condition
that t mod dt = first time (ps) was not being met because the first time was
a funny number. Have rectified it. Apologies for the inconvenience.
--
Maria G.
Technical University of Denmark
Copenhagen
--
gmx-use
Hi,
On 11/24/10 2:59 AM, lin hen wrote:
hi,
I am testing the dhfr benchmarks with gromacs 4.5.2
1. for the benchmarks: dhfr-solv-RF-1nm.bench and
dhfr-solv-RF-2nm.bench, set the steps = 1,
The GPU version running results shows as following:
./mdrun-gpu
Pre-simulation ~15s memtes
Quoting leila karami :
> Dear Justin
>
> Thank you so much for help.
>
> I used # symbol in where you said and problem was solved. a output was
> obtained with name summary_HBmap.dat.
> this file is as follows:
>
> #DonorAcceptor% Exist.
>
Quoting sagar barage :
> Dear sir,
>
>I am dealing with drug-Enzyme MD but during position restrained MD
> drug molecule moved from its original position of initial file.
>
> So what i can do for that?
>
Create a position restraint file for the ligand and restrain it as you would
anything
On 24/11/10 02:47, Mark Abraham wrote:
On 24/11/2010 5:04 AM, ms wrote:
On 23/11/10 17:00, Mark Abraham wrote:
There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.
Dear Justin
thanks for your attention
with chang of hbond.ndx file my problem was solved.
I have another question about g_hbond: if I want to obtain same information
(percentage of existence of each hbond during my trajectory) about water
mediated hydrogen bonds between protein and dna, for obta
Dear users,
I am applying an Electric Field along the z-axis to a system comprising a
protein nanopore and a PO4- in order to see if gets into the pore.
In some of the simulations the phosphate doesn't move on the opposite
direction of the applied field but in the same direction!
I wonder if anyon
Hi,
If you mean interactions bridged by a watermolecule, Protein-H2O-DNA,
then I don't know of any gromacs related tools for this. You need to
write your own tool for this. One way would be to multiply the existence
functions for hbonds between protein and water and the hbonds between
water a
Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
I followed the instruction on the website, I completed my make install and
this was the output:
GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possib
Dear Erik and Justin
Thank you so much for ypur help.
yes I mean water mediated hydrogen bonds (protein-H2O-dna).
since I'm beginner in perl script, please clarify your answer and explain
more. what is your mean of
existence functions exactly?
do using of -ins option in g_hbond tool help me?
Quoting Rossella Noschese :
> Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
> I followed the instruction on the website, I completed my make install and
> this was the output:
> GROMACS is installed under /usr/local/gromacs.
> Make sure to update your PATH and MANPATH to find the
> p
Dear gromacs users
I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.
Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg
files by details. Also, I want to know what is difference between p(t) in
hblife.xvg and c(t) in
hbac.xvg file? which of them is more suitable for HB li
ok, but when I type luck it says command not found, where's my mistake?
2010/11/24 Justin A. Lemkul
> Quoting Rossella Noschese :
>
> > Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
> > I followed the instruction on the website, I completed my make install
> and
> > this was the outp
Hi,
The -ins option is badly broken as far as I know. Don't expect it to
work anytime soon.
The hbmap.xpm depicts the existence functions h for all hydrogen bonds
as functuions of time. A red pixel means that the hydrogen bond is there
(h=1), white means that the hbond is broken (h=0). If yo
shahab shariati skrev 2010-11-24 16.24:
Dear gromacs users
I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.
Can anyone clarify last 2 columns in hblife.xvg and last 4 columns
hbac.xvg
files by details. Also, I want to know what is difference between p(t)
in hblife.xvg and c(t) in
hbac.xvg f
it was g_luck!!!it changed...ok, now it seems it wors!
Thanks
2010/11/24 Rossella Noschese
> ok, but when I type luck it says command not found, where's my mistake?
>
> 2010/11/24 Justin A. Lemkul
>
> Quoting Rossella Noschese :
>>
>> > Hi all, I'm trying to install gromacs.4.5.3 on fedora
Dear Erik
thanks.
thus -ac is only for determine the rate for hb breaking. is it true? or
there is other usable case for -ac option?
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support
Dear Erik
I'm confused. is there h(t) in hbmap.xpm file?
where is h(t)? which output file of g_hbond tool?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
o using of -ins option in g_hbond tool help me?
>
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> -- next part --
> An HTML attachment was scrubbed...
&g
On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote:
> Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
> I followed the instruction on the website, I completed my make install and
> this was the output:
> GROMACS is installed under /usr/local/gromacs.
> Make sure to update your PATH
Dear gromacs users,
I want to heat system from 0K till 300K. Than do equilibration dynamics in
water. I can not find any .mdp files where the system is gradually heated
from initial temperature (0K) till needed temperature. I can only find NVP
and NVT equilibration dynamics. Please can you advice
Quoting Olga Ivchenko :
> Dear gromacs users,
>
> I want to heat system from 0K till 300K. Than do equilibration dynamics in
> water. I can not find any .mdp files where the system is gradually heated
> from initial temperature (0K) till needed temperature. I can only find NVP
> and NVT equilibrat
Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds with
specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
grompp I got error about unrecognized bonds/angles. I made bond with MET SD
and FE of Heme. As earlier suggested on this list I wrote to get para
shahab shariati skrev 2010-11-24 16.45:
Dear Erik
thanks.
thus -ac is only for determine the rate for hb breaking. is it true?
or there is other usable case for -ac option?
And formation. And equillibrium constant.
--
---
Erik Marklund, PhD stude
Well, yes. The 'h' notation is never used in the xpm file. I just
borrowed it from Luzar and chandler. Every line in the xpm data is the
h(t) for a particular hydrogen bond.
Erik
leila karami skrev 2010-11-24 16.50:
Dear Erik
I'm confused. is there h(t) in hbmap.xpm file?
where is h(t)? whi
shahid nayeem skrev 2010-11-24 18.02:
Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds
with specbond.dat by pdb2gmx. After using editconf and genbox, when I
tried grompp I got error about unrecognized bonds/angles. I made bond
with MET SD and FE of Heme. As earlier
Hello GROMACS users,
I have a questions regarding how a Nose-Hoover thermostat works in non
equilibrium simulations
in GROMACS . If I apply some constant acceleration in the x direction, is
the thermostat applied
to all degrees of freedom or is it applied only in the y and z direction.
Thanks.
Ap
Dear users,
I was wondering if there is Martini topology available for simple formyl
(or aldehyde) group H - C = O. I would appreciate if somebody can direct
me to the place where such force field parameters are discussed.
Thanks,
George
--
George Khelashvili, Ph.D.
Department of Physiology
Erik Marklund wrote:
shahid nayeem skrev 2010-11-24 18.02:
Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds
with specbond.dat by pdb2gmx. After using editconf and genbox, when I
tried grompp I got error about unrecognized bonds/angles. I made bond
with MET SD an
Hi all
How to find the interfacial tension between two immiscible liquids in
gromacs?. how one should start abou it. any help is highly is appreciated.
Regards
Vinoth
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but
Met SD and FE bond is not there.
Shahid Nayeem
On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul wrote:
>
>
> Erik Marklund wrote:
>
>> shahid nayeem skrev 2010-11-24 18.02:
>>
>>> Dear all
>>> I am trying MD of cyt C con
Hi all
I want to calculate the interfacial tension of two immiscible liquids using
the surface tension option in gromacs. when i do that i am getting the error
message as
"One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than
Hi,
Is there a relationship between RMSD value obtained from the calculation and
Resolution value in PDB file?
Thanks in advance
--
Ahmet YILDIRIM
--
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http://www.gro
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