Mark,
> If you make your layer boundaries perpendicular to some axis then you can
> use position restraints on water oxygens that have non-zero force constants
> only with respect to that axis. Then relax the water position restraints
> before any others.
>
>
Yes, I've thought about this to appl
On 9/04/2012 7:27 PM, James Starlight wrote:
Mark,
If you make your layer boundaries perpendicular to some axis then
you can use position restraints on water oxygens that have
non-zero force constants only with respect to that axis. Then
relax the water position restraints before
Mark,
> Assuming you're raising your temperature during equilibration and then
> running at high temperature, then you don't want water moving into the
> receptor interior during equilibration for the same reason you didn't want
> water moving into the CCl4. And you're going to run further equ
priya thiyagarajan wrote:
hello sir ,
i got few basic doubts in dynamics..
while performing analysis, we are calculating rmsd and gyrate for
single molecule..
but in case of more molecules i.e by adding 20 molecules randomly using
genbox , when we perform analysis, rmsd value we are obta
Hi priya ,
I am also have same problem...
>From my limited experience ..
To solve these problem it is a good way to make
index file of particular group (or molecule )
and then measure there g_mindist, g_gyrate and g_hbond
You can get gyrate and hbond value for them...
Have a nice Day ...
With
hello sir,
thanks for your kind reply...
to study about micelle formation is it correct to use g_polystat. to
measure gyrate...
also i tried g_sas to find the solvent accessible surface and g_rdf..
but i dono how to interpret the result from the graph..
i gave calculation group and output grou
Thank you for your help, I tried to do as indicated in the link to send
to me, but it seems that it didn't change anything. Could you show me an
example, to better understand what I am doing wrong?
Thank you
Pierre THEVENET
Le 06/04/2012 17:19, Justin A. Lemkul a écrit :
pitheve...@free.f
Pierre THEVENET wrote:
Thank you for your help, I tried to do as indicated in the link to send
to me, but it seems that it didn't change anything. Could you show me an
example, to better understand what I am doing wrong?
It would be better for you to show us what you tried, along with what
priya thiyagarajan wrote:
hello sir,
thanks for your kind reply...
to study about micelle formation is it correct to use g_polystat. to
measure gyrate...
Probably not. There are a variety of other tools that are probably more
applicable. Check the manual, Chapter 8 and Appendix D, alo
James Starlight wrote:
Mark,
Assuming you're raising your temperature during equilibration and
then running at high temperature, then you don't want water moving
into the receptor interior during equilibration for the same reason
you didn't want water moving into the CCl4.
Dear Gmx Users,
I am running umbrella sampling on the cluster. The wall time is 72 hours so
I have to rerun my simulation every time. After first 72 hours I rerun my
simulation:
pbsexec mpiexec mdrun -s umbrella0.tpr -cpi umbrella0.cpt -append -deffnm
umbrella0 -pf pullf-umbrella0.xvg -px pullx-u
can anybody help me to make an .itp file for "Fe" I am trying to simulate
the
protein containing an Fe atom where it is needed.
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On 10/04/2012 4:58 AM, Kamalesh Roy wrote:
can anybody help me to make an .itp file for "Fe" I am trying to
simulate the
protein containing an Fe atom where it is needed.
See examples in ions.itp for the force field you are using. Hope that
you find parameters for Fe already exist for your f
On 10/04/2012 4:50 AM, Steven Neumann wrote:
Dear Gmx Users,
I am running umbrella sampling on the cluster. The wall time is 72
hours so I have to rerun my simulation every time. After first 72
hours I rerun my simulation:
pbsexec mpiexec mdrun -s umbrella0.tpr -cpi umbrella0.cpt -append
-d
Well, I did not change anything. I use Gromacs 4.5.4. Other windows work
fine, just 2 out of 30 failed like this. Shall I rerun it from the begining
then?
On Mon, Apr 9, 2012 at 8:04 PM, Mark Abraham wrote:
> On 10/04/2012 4:50 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am running umb
On 10/04/2012 5:07 AM, Steven Neumann wrote:
Well, I did not change anything. I use Gromacs 4.5.4. Other windows
work fine, just 2 out of 30 failed like this. Shall I rerun it from
the begining then?
OK, I'll spell it out then... if your file system might have been
transiently failing to serv
when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command in
my pdb file then i select AMBER99SB-ILDN force field (Lindorff-Larsen et
al., Proteins 78, 1950-58, 2010) this force field but a error massage came.
the massage is following:
There are 0 donors and 0 acceptors
There are 0 h
Bishwajit Das wrote:
when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command
in my pdb file then i select AMBER99SB-ILDN force field
(Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force field
but a error massage came.
the massage is following:
There are 0 donors a
Dear All,
I have a practice on the production MD according to the on-line lysozyme
tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html).
By the production MD step, I got 2 .trr file, one is md_0_1.trr, the other is
traj.trr fil
Acoot Brett wrote:
Dear All,
I have a practice on the production MD according to the on-line lysozyme
tutorial of *Justin Lemkul
*(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html).
By the production MD step, I got 2 .trr file, one is md_0_1.trr, t
Dear Sir/Madam,
I used the following steps to get the cosine content for my trajectories, could
you please kindly tell me how to interpret the results?
/usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v
/usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v eigenvec.
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