On 9/11/13 5:28 AM, Jernej Zidar wrote:
Dear Justin,
I followed your advice and started a gas-phase simulation. I removed the
solvent and simulated only the polymer molecule but I ended up with this error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|b
Pressure coupling with a single molecule (i.e. in the gas phase)
doesn't sound workable to me.
Mark
On Wed, Sep 11, 2013 at 11:28 AM, Jernej Zidar wrote:
> Dear Justin,
>
> I followed your advice and started a gas-phase simulation. I removed the
> solvent and simulated only the polymer molecu
Dear Justin,
I followed your advice and started a gas-phase simulation. I removed the
solvent and simulated only the polymer molecule but I ended up with this error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the
> On 9/2/13 9:43 PM, Jernej Zidar wrote:
>> Dear Justin,
>> I set the couple_intramol parameter to yes and rerun the free energy
>> simulations. mdrun was able to fully utilize all the cores in the
>> system but there's one issue. The free energy of solvation is vastly
>> different if the parame
On 9/2/13 9:43 PM, Jernej Zidar wrote:
Dear Justin,
I set the couple_intramol parameter to yes and rerun the free energy
simulations. mdrun was able to fully utilize all the cores in the
system but there's one issue. The free energy of solvation is vastly
different if the parameter is set to
Dear Justin,
I set the couple_intramol parameter to yes and rerun the free energy
simulations. mdrun was able to fully utilize all the cores in the
system but there's one issue. The free energy of solvation is vastly
different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol)
or 'yes'
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