actually get to use those 16 threads,
> assuming those aren't an emulation of some sort.
>
>
>
> On 6/24/2018 1:33 AM, Chhaya Singh wrote:
>
>> Hi,
>> I have attached the energy minimization mdp file.
>> please look through it .
t; quite a bit of scaling with system size beyond linear.
>
> Alex
>
>
>
> On 6/24/2018 1:04 AM, Chhaya Singh wrote:
>
>> Hi,
>>
>> I am trying to simulate a protein in an implicit solvent in groamcs using
>> amber ff99sb ildn .
>> the mdpfile tha
Hi,
I am trying to simulate a protein in an implicit solvent in groamcs using
amber ff99sb ildn .
the mdpfile that I am using is I have shown below:
integrator = md
dt = 0.001 ;0.005; ps !
nsteps = 500 ; total 5 ns.
nstlog =
I am running implicit solvent in gromacs . I am getting very less speed 300
ps per day. Is there any way to increase the speed.
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:
> I want to perform MD simulation using groamcs in implicit solvent. Can you
> help me which force field is compatible with which solvent I can take?
>
>
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I want to perform MD simulation using groamcs in implicit solvent. Can you
help me which force field is compatible with which solvent I can take?
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* Can't
I am running a simulation having protein in implicit solvent using amber
ff99sb forcefield and gbsa as solvent .
I am not able to use more than one cpu.
It always gives domain decomposition error if i use more than one cpu.
when i tried running using one cpu then it gave me this error :
"Fatal
