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:
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:
moleculetype CU1 is redefined
is it some thing wrong?
Below
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
Dear all,
In one of my simulations, total charge of the system is a noninteger number
(like +15.996). I neutralized it with 16 chlorine atoms. I am using periodic
boundary conditions. If I use the charge as it is, is it means infinite
negative total charge on the system?
Actually, when I che
12 matches
Mail list logo
