Robert:
With the original QM/MM implementation, free energy is currently not
possible (yet). From what you report, I guess that also with the CPMD
interface it does not work.
Lars
David Mobley wrote:
Robert,
I haven't heard of anyone who has done this in GROMACS yet. My hunch
is it will
Hello
I have a problem with Gromacs v3.3.1 installed in my $HOME on a SGI Altix
350 with 10 Itanium 2 64 bits processors runing SuSE Linux. I've tried to
run a QMMM optimization (with CPMD for the QM part) but even before CPMD is
called the memory start to go crazy (I saw the memory usage
Dear gmx-users,
I am trying to run a simulation of a pdb with DNA molecule.
I have give gromacs force fied and the error i found was,
There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms
chain #res #atoms
1 'A' 162 1245
2 'B' 162 1245
3 'C'21417
4
Subhrangshu Supakar wrote:
Hi All !
Can anyone help me in finding the minimum energy conformation after a
complete mdrum.
g_energy
Thanks,
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IIRC, the signature should embed the wiki page link now.
While at it, would it be possible to have an extra '-- '
(hypenhyphenspace) so when you reply to a comment, the signature is
automatically truncated (comes from the RFC, all mail clients should
follow it), and we don't get an increasing
You do not want to use the ffgmx forcefield. For simulating DNA and protein
i would use the amber force field. For more info on the ffamber ports see:
http://folding.stanford.edu/ffamber/
Tom
--On Wednesday, May 30, 2007 04:17:26 -0700 Alaguraj Veluchamy
[EMAIL PROTECTED] wrote:
Dear
Dear all
I am trying to run a simulation of a protein in popc.I
run grompp, there is error :
atomtype HC not found.where is wrong? itp or top
files.
thanks
Ready
for the edge of your seat?
Check out
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV protease
+ one ligand on a water box. I used the excellent protocol from John E.
Kerrigan (Drug-enzyme tutorial) in order to set up my simulation and
encountered some
Dear gmx-users:
I get a pdb file,and there are some water moleculers included in it.
Should I remove these water moleculers before I use genbox?
Any reply is appreciated.
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Rui Li wrote:
Dear gmx-users:
I get a pdb file,and there are some water moleculers included in it.
Should I remove these water moleculers before I use genbox?
Depends what those waters are doing. Waters embedded in an enzyme active
site should probably stay... but of course with such a
Hi Una,
Do the xaver.pdb and the md.trr correspond in terms of atom numbers?
The JACOBI error has to do with the fitting. The 'broken molecule'
thing is a warning, issued because you give a .pdb file which does not
contain information regarding connectivity, which coulod otherwise be
used to
With the original QM/MM implementation, free energy is currently not
possible (yet). From what you report, I guess that also with the CPMD
interface it does not work.
The CPMD interface is mostly plugged into the same setup as the other QM
interfaces, I was able to bypass the error by copying
Hi,
I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure
the main reason is that you cannot either mutate atom types or
decouple interactions gradually in the QM part of the system. Once
this is solved for a pure QM system it should be straightforward to
implement the
I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure the
main reason is that you cannot either mutate atom types or decouple
interactions gradually in the QM part of the system. Once this is solved
for a pure QM system it should be straightforward to implement the QM/MM
Robert fiske wrote:
I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure
the main reason is that you cannot either mutate atom types or
decouple interactions gradually in the QM part of the system. Once
this is solved for a pure QM system it should be straightforward to
Maybe I misunderstand you, but quantum programs are not likely to work with
fractional charges. If you do the charge change in the MM part it may be
possible (but it is definitely not implemented)
I did some tests with CPMD and it appeared to work with fractional charges,
I took a simple
mahbubeh zarrabi wrote:
Dear all
I am trying to run a simulation of a protein in popc.I
run grompp, there is error :
atomtype HC not found.where is wrong? itp or top
files.
thanks
try reading chapter 5.
--
David.
David
Actually, before submitting my question I checked google and it appears that
CPMD does allow partial charges, although I'm not sure if it's intended to
be used the way we want, so I'll ask that instead, but the answer to a CPMD
thread on partial charges is here:
Hi,
Does anyone have or know of a topology for a inorganic phosphate ion?
(PO4, -3)
Thanks!
Jason
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Please search the archive at
I think Erik is right, here. In a QM sense, what does it mean to have
an atom that is halfway in between, say, hydrogen and carbon?
You might want to look at what Wei Yang at Florida State has been
doing. If I remember correctly he has been making some efforts towards
QM/MM free energy
David Mobley wrote:
I think Erik is right, here. In a QM sense, what does it mean to have
an atom that is halfway in between, say, hydrogen and carbon?
You might want to look at what Wei Yang at Florida State has been
doing. If I remember correctly he has been making some efforts towards
QM/MM
Hello all,
I'm looking into performing dihedral PCA, but first I need to make an
appropiate index file. I would like to index the phi and psi angles for a
protein. I've searched in the archives but I didn't find anything clear
enough. I know I must specify four atoms for each, but could
Russell Green wrote:
Hello all,
I'm looking into performing dihedral PCA, but first I need to make an
appropiate index file. I would like to index the phi and psi angles for
a protein. I've searched in the archives but I didn't find anything
clear enough. I know I must specify four atoms
Dear gromacs users,
I have a quetion regarding using amber forcefield in gromacs.
I did the DNA and water interaction simulation. After the energy
minimization, the
original helix-structured DNA becomes two fragments. At this stage,
I assume that the simulation process is correct.
I used exactly
Hello
I have a problem with Gromacs v3.3.1 installed in my $HOME on a SGI Altix
350 with 10 Itanium 2 64 bits processors runing SuSE Linux. I've tried to
run a QMMM optimization (with CPMD for the QM part) but even before CPMD is
called the memory start to go crazy (I saw the memory usage
You want to name the atoms according to the atom types in ffamberXX.rtp
file. For an example of this for DNA see the dickerson.pdb provided in the
README directory of the ffamber port or this pdb can be downloaded on its
own from:
http://folding.stanford.edu/ffamber/
Tom
--On 30 May 2007
yes,there are some water molecules embedded in an enzyme active site.If I remove
them,and use genbox to get new water molecules , Does it influence the
simulation
result?
ÔÚÄúµÄÀ´ÐÅÖÐÔø¾Ìáµ½:
From: Mark Abraham [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Rui Li wrote:
yes,there are some water molecules embedded in an enzyme active site.If I remove
them,and use genbox to get new water molecules , Does it influence the
simulation
result?
Of course! If you have any appreciation for how enzymes work, you'll
quickly realise that anything in the
Hi Rui Li,
Everything you do influences the simulation results. Whether the
results are useful depends on the question.
Cheers,
Tsjerk
On 5/31/07, Rui Li [EMAIL PROTECTED] wrote:
yes,there are some water molecules embedded in an enzyme active site.If I remove
them,and use genbox to get new
FYI, best to keep these sort of discussions on the emailing list. That
way information is there for others to see and refer to in the future.
Thanks for replying to the querry.
My problem is unique, as I am setting up an AFM pulling in one
direction.
If I could keep the solute to one side of the
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