Dear all,
I hvae used ANTECHAMBER & GAFF of Amber generate a .prmtop and .prmcrd
of
a small molecular(XK263, a inhibitor of HIV-1 PR). I want to use ffamber99 in
Gromacs-3.3.1 to do a simulation of it, but I can't get the force field of the
molecular used in Gromacs.
On the Homepag
Mauro Puppett wrote:
Dear all,
I was running grompp with a symple phenol and I get this error message
Fatal error:
[ file "/usr/share/gromacs/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
I didn't make any change in spc.itp file so that sounds a bit strange
Adam Fraser wrote:
Hello,
I'm trying to get started working with a system of 2 hexadecane
molecules in water but I'm having some trouble.
I'm getting the following error when I run:
grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr
Program grompp, VERSION 3.3.2
Source code file
Hi,
On Oct 12, 2007, at 7:54 PM, Nickle Fan wrote:
Dear gmx-users:
I am working on incorporating a customized non-bonded interaction
into my simulation. I am trying to implementing it through the
tabulated interaction potential.
The manual says that the potential should be tabulated up t
Dear gmx-users:
I am working on incorporating a customized non-bonded interaction into my
simulation. I am trying to implementing it through the tabulated interaction
potential.
The manual says that the potential should be tabulated up to rc+1.0 nm (rc
is r_vdw or r_columb). Why is this necessary
Dear all,
I was running grompp with a symple phenol and I get this error message
Fatal error:
[ file "/usr/share/gromacs/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
I didn't make any change in spc.itp file so that sounds a bit strange.
Does anyone have an
Hello,
I'm trying to get started working with a system of 2 hexadecane molecules in
water but I'm having some trouble.
I'm getting the following error when I run:
grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr
Program grompp, VERSION 3.3.2
Source code file: readir.c, line: 794
2:35
>(Mnbf/s) (GFlops) (ns/day) (hour/ns)
>Performance: 13.021 3.143 5.574 4.306
>
>Best regards,
>Ivano
>--
>Ivano Eberini
>Gruppo di Studio per la Proteomica e la Struttura delle Proteine
>Dipartimento di Scienze F
Hi Zhenhai,
anyway the bonded(bond lengths, bond angles, and dihedral angles) and
nonbond energies can be calculated by hand with the geometry information
stored in pdb (xtc/trr) and the force field parameters.
Regards,
Jian Yin
Research Staff
E5-04-19
Singapore-MIT Alliance (SMA)
National Uni
Sampo Karkola wrote:
Hi Mark,
visualisation of the .trr file with vmd succeeded, but the original
problem remains.The -pbc cluster option did not do any better. The weird
thing is that after trjconv with -pbc cluster, -center tric and -ur
compact (or without the latter two) produces a traject
sarbani chattopadhyay wrote:
> hi,
> I am using gromacs to run MD simulations using "Intel dual core
> machine OSX (version
> 10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there
> any way to find
> whether the simulation process makes optimum usage of the 2 processors.
H
hi,
I am using gromacs to run MD simulations using "Intel dual core machine
OSX (version
10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there any
way to find
whether the simulation process makes optimum usage of the 2 processors.
Is there any command to direct the 'md
Hello, Xavier Periole
I have resolved my problem. Thanks for your help. You are so kind!
Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
China
Tel: 86-10-62773779
E-mail: [EMAIL PROTECTED]
2007-10-12
=== 2007-10-11 21:26:32 您在来信中写道：===
>--
Il giorno 12/ott/07, alle ore 11:29, David van der Spoel ha scritto:
Ivano Eberini wrote:
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-
fortran"?
the proof of the pu
...ok i misunderstood the com_t0 option. I'll try to introduce a virtual
particle without interactions, define a group on this and constrain the protein
distance to the particle.
Best
Martin
--
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten
Browser-Versionen downloaden: http://www.gmx.ne
Ivano Eberini wrote:
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-fortran"?
the proof of the pudding is in the eating.
please try it.
Thanks in advance for any sugg
An addition:
I have another trajectory with the same enzyme but another ligand with
exactly the same parameters and boxtype and simulated with the same
version of Gromacs and with the same machine at the same time. With this
one everything seems to work fine with g_angle and I also get correct
Hi there,
Maybe somebody has a hint what I did wrong there: I wanna constrain the com of
a protein to a fixed position in the box (e.g. to com_t0)?
I tried...
runtype = constraint
reference_group = Protein
reftype = com_t0
pulldim = Y Y Y
constraint_direction = 1.0 1.0 1.0
ngroups = 1
group_1 =
Hi Mark,
visualisation of the .trr file with vmd succeeded, but the original
problem remains.The -pbc cluster option did not do any better. The weird
thing is that after trjconv with -pbc cluster, -center tric and -ur
compact (or without the latter two) produces a trajectory with the
ligand i
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-
fortran"?
Thanks in advance for any suggestion.
Best regards,
Ivano
--
Ivano Eberini
Gruppo di Studio per la Proteomica
20 matches
Mail list logo
