On 8/17/15 9:51 PM, Roshan Shrestha wrote:
I am about to burst into tears now, since I am unable to get in touch with
you guys. My problem is regarding the installation of gromacs 4.6.1, I
followed exactly what was said in
https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-
Dear Roshan,
Don't let it get to you! Gromacs is frustrating for all people relatively
new. Sorry I can't help with your problem as I am not exactly an expert
here but I am trying to provide moral support: hang in there! People are
very helpful in the gromacs community and I am sure you will be ab
I am about to burst into tears now, since I am unable to get in touch with
you guys. My problem is regarding the installation of gromacs 4.6.1, I
followed exactly what was said in
https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-linux-users/
I followed with success till the l
Hi,
Under the assumptions underlying the drift tolerance, yes. (It's actually
slightly better than advertised, because of the use of discretized
clusters.) At some point, the numerical perturbation from the constraint
implementation dominates, as you can read about in the PDF reference manual
and
Sorry, I mean:
If I use double precision gmx mdrun and constraint h-bonds, can I expect
1.135 rlist to give a drift in total energy as small as the one in the
table?
On Mon, Aug 17, 2015 at 5:07 PM, Johnny Lu wrote:
> Thank you for the advices.
>
> I tried setting different varlet buffer drift i
Thank you for the advices.
I tried setting different varlet buffer drift in the 1st equilibration run
(nvt) for 5 seconds.
>From the log file of mdrun, I get:
rlistverlet-buffer-drift
1.090.05
1.1140.005
1.1350.0005 <=
1.1730.05
1.234
On 8/17/15 2:02 PM, Johnny Lu wrote:
Dear Users,
Hi.
Box vector length:
3.448, 3.448, 3.448 nm dodecahedron.
(Box volume is 28.98 nm^3)
Diameter of tripeptide:
1.248 nm
Volume of tripeptide:
0.35503 nm^3 (from genbox output)
Short range Neighbor list cut-off:
On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote:
Hi all, I have a crystallographic PDB file which comes some waters molecules.
I want to run an MD simulation which includes those water molecules. After
generating the topology file (which includes the waters) and defining the box
shape,
On 8/17/15 2:49 AM, Mehrnoosh Hazrati wrote:
Dear all,
hi
in the case of writing the .itp file, is it correct to use different
functions type for dihedrals?!
Normally force fields don't mix different function types. If you're trying to
hack together different parameter sets, this is unwi
On 8/16/15 12:38 PM, elham tazikeh wrote:
Dear GMX Users
is there anyone to help me in g_mmpbsa using for binding free energy
calculation
i have questions about *.mdp files as polar.mdp or
for instance: what is the value of pdie in protein-ligand combinations
i really appriciate for any he
I haven't tried that before.
May be you can open the .gro files before and after genbox with a text
editor.
Then, check those water molecules?
Those water molecules might have the same residue id.
On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz <
cos...@cim.sld.cu> wrote:
> Hi al
Dear Users,
Hi.
Box vector length:
3.448, 3.448, 3.448 nm dodecahedron.
(Box volume is 28.98 nm^3)
Diameter of tripeptide:
1.248 nm
Volume of tripeptide:
0.35503 nm^3 (from genbox output)
Short range Neighbor list cut-off:
1.1 nm (set manually by rlist=1.1)
Other
Hi all,
I have a crystallographic PDB file which comes some waters molecules. I want to
run an MD simulation which includes those water molecules. After generating the
topology file (which includes the waters) and defining the box shape, I fill
the box with solvent using genbox. At this point it
If you mean more than one term for a single dihedral, that would require
function type 9 (see section 4.2.12 in the manual). Otherwise, if you
specify a single dihedral more than once with different function type each
time, I'm not sure what GROMACS would do.
Hope this helps.
Victor
2015-08-17
Hi,
On Mon, Aug 17, 2015 at 11:23 AM Jernej Zidar
wrote:
> Hi Mark,
> I will send you the files.
>
Unfortunately I can see no likely source of problems in them. A fresh build
of 5.1 works fine for me.
I managed to solve the issue by replacing the content of the
> ~/gromacs-5.1/src/gromacs/
Hi Mark,
I will send you the files.
I managed to solve the issue by replacing the content of the
~/gromacs-5.1/src/gromacs/simd directory with files from Gromacs
5.0.6. Still curious about what could have caused such an issue.
Best,
Jernej
>
> Hi,
>
> That all seems wildly unlikely, particul
Hi,
That all seems wildly unlikely, particularly as you say you can compile
earlier GROMACS versions with the same toolchain. The errors are caused by
the compiler interpreting gmx_unused as a variable name, instead of a
portable way to suppress compiler warnings about variables that are unused
on
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