Hi,
On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham wrote:
> Jamie Seyed wrote:
>>
>> Dear all,
>> I performed an md simulation but it crashed at the beginning because
>> according to it "system was exploding". Also when I tried to see the
>> system
>> by ngmx, there was no water anymore and it was
Hi,
If you turn all bonds to constraints, and your system is infinitely
periodic, you probably don't even need impropers. The bond lengths can
only be satisfied in the plane. Adding impropers, straining your
molecule further into the configuration you think is proper, adds
forces that inevitable c
Dear all,
I am going to run some MD simulation of a protein bearing a copper cluster (3
Cu2+ nominally charge
2+) coordinates to histidine residues. As far as concerning the importance of
this cluster in the
enzymatic activity (this would require QM/MM), my issue is how to interpret the
"whole"
Hi Andrea,
You're probably best off 'fixing' the copper to the protein, meaning
introducing bonds at least (harmonic, type 6?). With these bonds you
can to some degree account for the effects of polarization and such on
the interatomic distances, which are likely more difficult to model
reparamete
Dear Andrea,
Which restraints did you use?
I've ran simulations on a similar system (Zn2+ coordinated to
histidines) with NMR restraints as implemented in Gromacs and it worked
fine.
Best regards,
Ran.
andrea spitaleri wrote:
> Dear all,
> I am going to run some MD simulation of a protein bearin
Hi Tsjerk,
thanks for the usual useful suggestions! Probably I will go for that, add an
harmonic bonds between
Cu2+ and N-HIS and I will think how to hand the charges too.
Probably this is the less worst solution for now.
Thank a lot,
Regards
andrea
Tsjerk Wassenaar wrote:
> Hi Andrea,
>
> Yo
Dear all, Thanks for all comments. I will check again all steps for my
previous simulation with right files (according to Mark) and then I will let
you know if I got the same problem (I am not working on proteins).
Another question:
--After energy minimization step for in-vacuo run, Should I do sti
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step, change coulomb type ,... but
Jamie Seyed wrote:
Dear all, Thanks for all comments. I will check again all steps for my
previous simulation with right files (according to Mark) and then I will
let you know if I got the same problem (I am not working on proteins).
Another question:
--After energy minimization step for in-v
Janne, Jussi,
Thank you very much!
Vitaly
On Wed, Aug 12, 2009 at 11:35 AM, Janne Blomqvist wrote:
> Vitaly V. Chaban wrote:
>>
>> On the same topic, I have a question to the community: does anybody
>> try to make *so*-library (or *dll* on windows) of xdrfile in order to
>> use with other progra
Hello all,
I got a question when I read the the manual chapter for the single sum virial
(p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here
also depend on index j? I think delta is zero when particle i and j are close.
And delta can be something else when any x/y/z c
Hi Lanyuan Lu,
It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at:
http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/
Cheers,
Tsjerk
2009/8/12 LuLanyuan :
> Hello all,
> I got a question when I read the the manual chapter for the single sum
> virial (p19
Hi There,
I have some problems installing gromacs on the linux server.
fftw installed with no error, but when I install gromacs,
I got the following error:
*
/bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer
-finline-functions -Wal
That's cool. Thanks a lot!
Lanyuan
> Date: Wed, 12 Aug 2009 22:01:14 +0200
> Subject: Re: [gmx-users] A question regarding single sum virial
> From: tsje...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi Lanyuan Lu,
>
> It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available
Hello,
Unfortunately I still don't understand the equations in the manual after
reading Chapter 2 of Hendrik Bekker's dissertation. In that chapter, the virial
is expressed as A+B+C.
Here A+B is the r_i*F_i stuff, which can be considered as the virial without
considering PBC. And the third ter
Dear all,
--
Shuangxing Dai
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to th
Dear all, I was trying to use Xcode to debug the file mdrun and hope to
trace the flow of source file by running a simple case. There is a tutorial
for using Xcode to debug a package named apbs, which is very like Gromacs,
here:
http://www.macresearch.org/tutorial-introducing-xcode-30-organizer
I
Hi Mark,
I do have a paper in my possession that provides a first principles
calculation of the adsorption energy of ammonia on graphene. I was
planning on using this paper to compare the adsorption energy to the
vibrational energy of the individual atoms in the graphene lattice. But
how do I
Hi David,
Thank you for your comments.
The bulk of the graphene sheet is not polarized in the absence of a
connection to electrodes. In some experiments on graphene adsorption,
they show significant adsorption of ammonia, but in these experiments
they connected the graphene sheet to electrodes
Hi gmx-users,
I am building a polymer and I've added the monomer unit to the .rtp file. The
final structure appears with an undesired bond between the monomer units at the
extremes of the polymer.
How can I prevent the monomers at the end forming the bond?
I have read other post like
http://w
nicegromacs wrote:
Hi gmx-users,
I am building a polymer and I've added the monomer unit to the
.rtp file. The final structure appears with an undesired bond between
the monomer units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?
Bonds that a
Hello,
In an earlier message, it was stated that topolbuild generated topologies
with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version
1.2.2), and the only files in the "dat/gromacs" directory are for the force
fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-A
Shuangxing Dai wrote:
Dear all, I was trying to use Xcode to debug the file mdrun and hope to
trace the flow of source file by running a simple case. There is a tutorial
for using Xcode to debug a package named apbs, which is very like Gromacs,
here:
http://www.macresearch.org/tutorial-introduc
Morteza Khabiri wrote:
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step, chan
Hi,
the bad bond appear in the topology (.top) file.
veduardo.
Lab. de Fisicoquímica Molecular
Facultas de Ciencias
Universidad de Chile
From: nicegromacs
Sent: Wednesday, August 12, 2009 8:28 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] bad bond in polymer
Hi gmx-users,
I am
nicegromacs wrote:
Hi,
the bad bond appear in the topology (.top) file.
Then it is something you have added. If you want any useful advice, post the
.rtp entries you are using.
-Justin
veduardo.
Lab. de Fisicoquímica Molecular
Facultas de Ciencias
Universidad de Chile
*From
Darrell Koskinen wrote:
Hi Mark,
I do have a paper in my possession that provides a first principles
calculation of the adsorption energy of ammonia on graphene. I was
planning on using this paper to compare the adsorption energy to the
vibrational energy of the individual atoms in the graphen
st wrote:
> Hi There,
>
> I have some problems installing gromacs on the linux server.
>
> fftw installed with no error, but when I install gromacs,
> I got the following error:
> *
> /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointe
Hi,
the .rtp
[ POL ]
[ atoms ]
CAA CH30.000
CAB CH20.000
CAC CH20.000
CAD CH20.000
CAE CH20.000
CAF CH20.000
CAG CH10.000
CAH CH20.041
CAI CH10.107
CAJC0.352
OAK OM -0.750
OAL OM -0.750
CAM CH20.044
CAN
nicegromacs wrote:
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least one
terminus of your polymer chain. You may find this post useful:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the st
I am working with a membrane protein dimer, each monomer being
constituted of a single helix. I have already studied the effect of
point mutations on the structure and the free energy involved by using
FEP. But I have read a paper in which the author has done PMF
calculations in order to calculate
Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In the
pdb file They have the same order (DRG DR0 DR1). But when tried with
pdb2gmx then I have the error:
Fatal error:
In the .rtp file in residue DR1 at line:
CF1 CH3 0 1
I changed the order of monomers to DR0 DRG DR1
Justin A. Lemkul wrote:
nicegromacs wrote:
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
one terminus of your polymer chain. You may find this post useful:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
I don't have any relevan
nicegromacs wrote:
Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In
the pdb file They have the same order (DRG DR0 DR1). But when tried
with pdb2gmx then I have the error:
Fatal error:
In the .rtp file in residue DR1 at line:
CF1 CH3 0 1
There is no such line in
--- On Thu, 13/8/09, st wrote:
From: st
Subject: [gmx-users] problem installing gromacs
To: gmx-users@gromacs.org
Date: Thursday, 13 August, 2009, 1:42 AM
Hi There,
I have some problems
installing gromacs on the linux server.
fftw installed with no error, but when I install
gromacs
Samik Bhattacharya wrote:
--- On Thu, 13/8/09, st wrote:
From: st
Subject: [gmx-users] problem installing gromacs
To: gmx-users@gromacs.org
Date: Thursday, 13 August, 2009, 1:42 AM
Hi There,
I have some problems
installing gromacs on the linux server.
fftw installed with no error,
Der all,
I'd like to know if any has had experience in using GROMACS for modeling
exotic metal species like Gadolinium(III) and Indium(III)? My system is
actually an Indium(III) ion coupled to DTPA
(diethylenetriaminepentaacetate), an octadentate ligand forms bonds with
metals through three atom
Hello everyone
I am doing MD on a protein, and everything including the EM seems to go well.
When I start to do the position restrained MD (or even directly the MD without
doing the PR MD), I get a "Segmentation fault".
when a doing EM,I set nsteps = 500,because i just want to go though the
?? wrote:
Hello everyone
I am doing MD on a protein, and everything including the EM seems to go well. When I start to do the position restrained MD (or even directly the MD without doing the PR MD), I get a "Segmentation fault".
when a doing EM,I set nsteps = 500,because i just want to g
Lili Peng wrote:
Der all,
I'd like to know if any has had experience in using GROMACS for modeling
exotic metal species like Gadolinium(III) and Indium(III)? My system is
actually an Indium(III) ion coupled to DTPA
(diethylenetriaminepentaacetate), an octadentate ligand forms bonds with
me
40 matches
Mail list logo
