On 01/25/11, ahmet yıldırım wrote:
> Dear Mark,
>
> A million thanks. Problem is solved.
> Finally,
> Select a continuous group of solvent molecules:
> ...
> Group 12 ( Water) has 126219 elements
> Group 13 ( SOL) has 126219 elements
>
>
> Which one should I choose
Dear Mark,
A million thanks. Problem is solved.
Finally,
Select a continuous group of solvent molecules:
...
Group12 ( Water) has 126219 elements
Group13 (SOL) has 126219 elements
Which one should I choose 12 or 13?
*Final topol.top file:
*;File 'topol.top' was
On 01/25/11, ahmet yıldırım wrote:
> Dear Mark and Emanuel,
>
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any
> problem about these files?
>
No. So one of the other #include files is erroneously defining ion molecule
types. See www.gromacs.org/Documentation/In
Dear Mark and Emanuel,
I am sending the ions.tip and the topol.top files. Everything seems ok. Any
problem about these files?
By the way, I am using the Gromacs 4.5.3.
Force Field 43a1
25 Ocak 2011 12:03 tarihinde Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> yazdı:
> Hello,
>
> You h
Hello,
You have to look into your ions.itp which is included in your top-file by
#include ions.itp.
There all the types of ions have to be defined.
The atom-types which you can see in the ions.itp, you will
find in the ff"your-forcefield".itp where your atomtypes are defined.
On top of your .top f
On 01/25/11, ahmet yıldırım wrote:
> Dear Mark,
>
> I looked at gromacs mail list but I could not find a proper solution .What
> should I add to the .top file? Please look at the following reconstructed1
> .top and reconstructed1 .top files
>
>
> I have error as the following reconstructed
Dear Mark,
I looked at gromacs mail list but I could not find a proper solution
.Whatshould
I add to the .top file? Please look at the following reconstructed1 .top and
reconstructed1 .top files
I have error as the following reconstructed1 .top file:
*Fatal error:*
moleculetype CU1 is redefined
On 01/25/11, ahmet yıldırım wrote:
> Hi,
>
> In my simulation, total charge of the system is a noninteger number (System
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
> atoms.
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> Fatal error:
Serdar.
If the "real charge" of your system is not zero and you are using PME, then
PME code will take account for any non-zero charge on the system and
neutralize it with an uniform background charge (
http://wiki.gromacs.org/index.php/Errors).
If your system is composed by a protein, then try fi
Sometimes when grompp reports the total charge, it shows up as a non-integer and
can sometimes be attributed to a round-off error. Just to be sure, check your
topology to make sure you have integer charges on all components of your system.
-Justin
serdar durdagi wrote:
Dear all,
In one o
10 matches
Mail list logo
