On 11/16/11 2:09 PM, James Starlight wrote:
Dear Gromacs Users!
I wounder to know how I can obtain .gro file from the unfinished ( e.g
termenated or crashed ) MDrun. I Have only trajectory of my system in .trr
How I can obtain gro file from that .trr wich would correspond to the
last simulat
Dear Gromacs Users!
I wounder to know how I can obtain .gro file from the unfinished ( e.g
termenated or crashed ) MDrun. I Have only trajectory of my system in .trr
How I can obtain gro file from that .trr wich would correspond to the last
simulation time before my simulation was stoped ?
I've
>
>
> --
>
> Message: 2
> Date: Tue, 15 Nov 2011 17:53:19 +0530
> From: shahid nayeem
> Subject: [gmx-users] RMSD
> To: Discussion list for GROMACS users
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1&q
Hi Mark,
Sorry my last mail was incomplete...here is the complete one!
> On 16/11/2011 1:18 AM, Harpreet Basra wrote:
> > Hi Mark,
> >
> > Thanks for the quick reply. But i have already done what u suggested.
> >
> >
> >
> > On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > > Hi
> >
> On 16/11/2011 1:18 AM, Harpreet Basra wrote:
> > Hi Mark,
> >
> > Thanks for the quick reply. But i have already done what u suggested.
> >
> >
> >
> > On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > > Hi
> > > I am still stuck with same problem of obtaining positive potential
> >
On 16/11/2011 5:46 AM, Nilesh Dhumal wrote:
Hello,
I am trying to calculate the dihedral angle between four points.
I considered two planes (ABC& BCD) and calculate the dot products of two
normals (n1 and n2)to these plane.
theta=cos-1(n1.n2)
I compared theeta values of dihedral angle with a
Thanks, I will try to figure it out.
On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham wrote:
> On 16/11/2011 2:45 PM, Liu, Liang wrote:
>
> Thanks for help.
> If I have more atoms and they can interact each other or itself, like PP,
> PC, PN, CP, CN, CC How's the energygrp_table looking like?
On 16/11/2011 2:45 PM, Liu, Liang wrote:
Thanks for help.
If I have more atoms and they can interact each other or itself, like
PP, PC, PN, CP, CN, CC How's the energygrp_table looking like?
I know there should be a option in the grompp, but how to do that?
See manual sections 7.3.12 and
Thanks for help.
If I have more atoms and they can interact each other or itself, like PP,
PC, PN, CP, CN, CC How's the energygrp_table looking like?
I know there should be a option in the grompp, but how to do that? And how
to generate the index file? I am sorry for so many questions, I am re
>From your system information, I understand that you need to specify
tabulated potentials between atoms P and P, and between atoms C and P, and
so on.
To achieve this, you need to create energy groups with atom types P and C,
and specify energygrp_table options in the grompp such as following
...
I am trying to use a serial of tabulated potentials, which are the
functions of the distance between atoms and the names are table.xvg,
table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some
RNA structures.
The procedure I apply is as following:
pdb2gmx -f rna.pdb -o conf.pdb -f
Hello,
I am trying to calculate the dihedral angle between four points.
I considered two planes (ABC & BCD) and calculate the dot products of two
normals (n1 and n2)to these plane.
theta=cos-1(n1.n2)
I compared theeta values of dihedral angle with ampac and some values are
negative. I am geting
shilpa yadahalli wrote:
Dear Justin,
Thanks alot for your such a fast reply.
I will surely go thr the page mentioned by you.
Thanks-alot again.,
Given this information, I still think everything is completely normal.
-Justin
Here is my mpt.mdp file: ( i start from output of nvt equilibrati
shilpa yadahalli wrote:
After doing NPT simulation I plot pressure and density. How much
pressure change is considered as normal? I'm getting pressure change +/-
500 bar, after doing NPT equilibration for most of my proteins. And for
one of the protein it is as high as +/- 1000 bar.
Can anybo
After doing NPT simulation I plot pressure and density. How much pressure
change is
considered as normal? I'm getting pressure change +/- 500 bar, after doing NPT
equilibration for most of my proteins. And for one of the protein it is as high
as +/- 1000 bar.
Can anybody tell me what is the Nor
The tabulated potentials I am using is non-bonded interactions. The
question is the application of these potentials will only modify the force
field, e.g. amber03, or will take place of the force field?
On Mon, Nov 14, 2011 at 6:40 PM, Mark Abraham wrote:
> On 15/11/2011 9:33 AM, Liu, Liang wr
On 16/11/2011 1:18 AM, Harpreet Basra wrote:
Hi Mark,
Thanks for the quick reply. But i have already done what u suggested.
On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> Hi
> I am still stuck with same problem of obtaining positive potential
> energy.
> >>On 11/11/2011 5:
Hi Mark,
Thanks for the quick reply. But i have already done what u suggested.
>
> On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > Hi
> > I am still stuck with same problem of obtaining positive potential
> > energy.
> > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> > >> Hi
> > >>
> > >> I a
In any case, if you really want to see flexibility then you need RMSF and not
RMSD as the later will only tell you about how similar is the configuration of
a sidechain compared to a reference frame. If that is still what you want i
think VMD has a tool for that in the timeline plugin.
rega
On 11/15/11 8:23 PM, shahid nayeem wrote:
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I
want to get the flexible and rigid regions of protein chain during
simulation. g_rmsf does not gives me this plot.
Please help
shahid Nayeem
Try g_rmsf -res , it could be
sai nitin wrote:
Hi all,
I just started learning molecular dynamics analysis of protein-ligand
complexes to do this i downloaded GROMACS 4.5.5 and tried to install
according to Manual instructions executed following commands..
./configure
make (when i executed this command it is showing
Hi all,
I just started learning molecular dynamics analysis of protein-ligand
complexes to do this i downloaded GROMACS 4.5.5 and tried to install
according to Manual instructions executed following commands..
./configure
make (when i executed this command it is showing following error *** No
t
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I want
to get the flexible and rigid regions of protein chain during simulation.
g_rmsf does not gives me this plot.
Please help
shahid Nayeem
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http://lists.gromacs.org/mai
arun kumar wrote:
Dear friends,
i had a problem while running the of protein-ligand complex simulation,
in which i have generated the ligand toplogy by using online Prodrg
server and iam using gromos 96.1froce field.
there was an note and an error during minimization
NOTE 2 [file trp.top]
Dear friends,
i had a problem while running the of protein-ligand complex simulation, in
which i have generated the ligand toplogy by using online Prodrg server and
iam using gromos 96.1froce field.
there was an note and an error during minimization
NOTE 2 [file trp.top]:
The largest charge gr
So, I also check the literature, for water, using flexible SPC model, in
Buckingham potential form
How do I use the Buckingham potential form for flexible SPC model?
rewriting the itp for water?
Best
XJ
在 2011年11月15日 下午12:12，xiaojing gong 写道：
> Many thanks
>
>
> 2011/11/15 Mark Abraham
Many thanks
2011/11/15 Mark Abraham
> On 15/11/2011 9:17 PM, xiaojing gong wrote:
>
> ...I am not sure...Do you have some suggestions?
>
>
> No. The two functional forms are incompatible. GROMACS only allows you to
> define one set of nonbonded parameters, so you can only use one functi
On 15/11/2011 9:17 PM, xiaojing gong wrote:
...I am not sure...Do you have some suggestions?
No. The two functional forms are incompatible. GROMACS only allows you
to define one set of nonbonded parameters, so you can only use one
functional form in a given simulation. This is fixed i
...I am not sure...Do you have some suggestions?
在 2011年11月15日 上午11:05，Mark Abraham 写道：
> On 15/11/2011 9:03 PM, xiaojing gong wrote:
>
> Many thanks for reply.
> Another question, If I use Buckingham potential for CNT, and I want to
> simulate CNT and water, shall I also transfer the SP
On 15/11/2011 9:03 PM, xiaojing gong wrote:
> Many thanks for reply.
> Another question, If I use Buckingham potential for CNT, and I want to
> simulate CNT and water, shall I also transfer the SPC.itp from LJ to
> Buckingham potential?
>
> The most important is how to transfer?
> I will appreciate
Many thanks for reply.
Another question, If I use Buckingham potential for CNT, and I want to
simulate CNT and water, shall I also transfer the SPC.itp from LJ to
Buckingham potential?
The most important is how to transfer?
I will appreciate it if you can give me any suggestions.
Best
XJ
2011/11
Hi,
I am interested in the structure of a protein where some asparagine
residues are N-glycosylated by N-Acetylglucosamine (NAG). As a first
step I tried to model NAG itself (see e.g.
http://xray.bmc.uu.se/hicup/NAG/index.html) in the OPLS-AA force field
using implicit solvation; this has invol
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