On 11/27/12 4:31 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization (after shrinking), getting error like this.
Fatal error:
Invalid line in system_shrink26.gro for atom 8703:
6.4140 6.44350 6.59650.why this er
Probably..there is a problem in spacing at the bottom of your gro file. The
line mentioning the vectors should be like this
eg:,
5012OBC49 47 1.088 1.094 2.775
0.0 0.0 0.0
On Tue, Nov 27, 2012 at 3:01 PM, Shine A wrote:
> Sir,
>
>I am studying the dynamics o
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization (after shrinking), getting error like this.
Fatal error:
Invalid line in system_shrink26.gro for atom 8703:
6.4140 6.44350 6.59650.why this error?plz give me a solution to
overcome it.
-
On 10/11/12 10:27 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
Change the number of nodes or mdrun opti
nishap.pa...@utoronto.ca wrote:
I have a question regarding the simulations that I am running. I tried
creating a pdb file with one methane and water molecules, but the system
keeps showing 'bad contact' error when I run the minimization step and I
don't understand what I am doing wrong.
Thi
Hi Nisha,
you say "And it runs minimization with bad contact errors", but I don't see any indication of that error message here.
Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information
as output by gromacs.
Chris.
-- origi
I have a question regarding the simulations that I am running. I tried
creating a pdb file with one methane and water molecules, but the
system keeps showing 'bad contact' error when I run the minimization
step and I don't understand what I am doing wrong.
This is my methane file :
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