On 1/01/2012 9:38 PM, banafsheh mehrazma wrote:
Hi everyone,
I am studying a paper about a DNA simulation using Gromacs and I
encountered this in ion addition step:
Na+ were added by replacing a solvent molecule at ca. 6 Å
from the phosphorus in the direction of the bisector of the angle
?O1P-
niaz poorgholami wrote:
Dear all
I am using Gromacs 4.5.3 to simulate a system including:
CNT+water+surfactant and I want to
use opls force field for my whole system.
so far I have done following things:
1.I copied oplsaa.ff folder in my working directory.
2.I added following lines to atomnam
Hey Mark, thanks for your help. It was extremely useful, now it's solved
and running XD.
Nice year friend :)
Willian Felix
On Sat, Dec 31, 2011 at 10:36 PM, Mark Abraham wrote:
> On 31/12/2011 11:58 PM, Willian Pereira Felix wrote:
>
> Hello buddies,
>
> I'm a very beginner in gromacs and I j
Dear all
I am using Gromacs 4.5.3 to simulate a system including:
CNT+water+surfactant and I want to
use opls force field for my whole system.
so far I have done following things:
1.I copied oplsaa.ff folder in my working directory.
2.I added following lines to atomname2type.n2t
Copls_9950
On 2/01/2012 12:35 AM, Saba Ferdous wrote:
Dear Gromacs Experts,
I am having problem in execution of a command in Gromacs,
thats when i use dssp for secondary structure analysis.
it gives error:
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Reading file md_0_10.tpr, VERSION 4.5.
Dear Gromacs Experts,
I am having problem in execution of a command in Gromacs,
thats when i use dssp for secondary structure analysis.
it gives error:
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Segmentation fault (core
Hi everyone,
I am studying a paper about a DNA simulation using Gromacs and I encountered
this in ion addition step:
Na+ were added by replacing a solvent molecule at ca. 6 Å
from the phosphorus in the direction of the bisector of the angle
∠O1P-P-O2P (O1P and O2P being the phosphate nonbridg
On 2012-01-01 10:11, parto haghighi wrote:
Dear GMX usesr,
I have to do charge fitting for a small molecule like ethanol.
I have applied PRODRG to generate .gro and .itp for ethanol but it has
wrong atomic charge.
To correct it I have to use gromos 43a1 force field parameters to assign
charges o
Dear GMX usesr,
I have to do charge fitting for a small molecule like ethanol.
I have applied PRODRG to generate .gro and .itp for ethanol but it has
wrong atomic charge.
To correct it I have to use gromos 43a1 force field parameters to assign
charges on each atom (Is it right?)
I have red a pape
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