Thanks a lot. I could set up and perform the simulations using position
restraints and md+nose-hoover thermostat as suggested by Justin. The
combination seems to yield the correct canonical ensembles.
Equilibration with Berendsen barostat (with integrator=sd and
refcoord-scaling = com) does not se
On Thu, Aug 22, 2013 at 12:51 AM, HANNIBAL LECTER
wrote:
> Thanks. I am not interested in the real physics of the freezegroups as I am
> assuming the fluctuations are negligible in the timescale of the
> fluctuations of the non-freeze groups.
That may be true in the case where the non-interesting
Thanks. I am not interested in the real physics of the freezegroups as I am
assuming the fluctuations are negligible in the timescale of the
fluctuations of the non-freeze groups. I thought that the langevin
thermostat is quite effective in this case just to ensure that there is no
net heat flow fr
On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER
wrote:
> I am not sure what is the problem with using NPT, constraints and
> freezegroups. Unless there is some fundamental issue (which I cannot think
> of) one should in principle be able to run NPT with the CNT system by
> freezing the CNT group
On 8/21/13 4:22 PM, HANNIBAL LECTER wrote:
I am not sure what is the problem with using NPT, constraints and
freezegroups. Unless there is some fundamental issue (which I cannot think
of) one should in principle be able to run NPT with the CNT system by
freezing the CNT group. I am using sd wit
I am not sure what is the problem with using NPT, constraints and
freezegroups. Unless there is some fundamental issue (which I cannot think
of) one should in principle be able to run NPT with the CNT system by
freezing the CNT group. I am using sd with LINCS to constraint the bonds.
However, if md
Interestingly, removing position restraints does not have much of an impact.
On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul wrote:
>
>
> On 8/19/13 11:58 AM, HANNIBAL LECTER wrote:
>
>> I usually use 1.0 for my systems and I get the correct values for the
>> temperatures. If I couple it as a sy
On 8/19/13 11:58 AM, HANNIBAL LECTER wrote:
I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple it as a system, the low T-CNT yields a different
value than the target 300K.
What about changing the integrator to md? What happens if you remove restr
I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple it as a system, the low T-CNT yields a different
value than the target 300K.
On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul wrote:
>
>
> On 8/19/13 11:42 AM, HANNIBAL LECTER wrote:
>
>> Thanks Justi
On 8/19/13 11:42 AM, HANNIBAL LECTER wrote:
Thanks Justin.
I am not sure how it is fundamentally incompatible. Especially with
refcoord-scaling = com. Can you please provide with some more input on that?
The refcoord-scaling option doesn't matter with frozen groups. Anything that is
froze
I am performing NPT here but this artifact is independent of whether one is
using NPT or NVT.
On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER <
hanniballecte...@gmail.com> wrote:
> Thanks Justin.
>
> I am not sure how it is fundamentally incompatible. Especially with
> refcoord-scaling = com.
Thanks Justin.
I am not sure how it is fundamentally incompatible. Especially with
refcoord-scaling = com. Can you please provide with some more input on that?
The outputs are from g_energy.
Here is the .mdp file.
define = -DPOSRES_CNT
constraints = all-bonds
pbc
On 8/19/13 11:32 AM, HANNIBAL LECTER wrote:
Hi,
I have been performing NPT simulations with CNT, Protein and water.
However, when I freeze the CNT, the system crashes with segmentation fault.
That is to be expected. Frozen atoms and pressure coupling are fundamentally
incompatible.
If
Hi,
I have been performing NPT simulations with CNT, Protein and water.
However, when I freeze the CNT, the system crashes with segmentation fault.
If I use position restraints, the temperature of the system is lower than
what it is expected to be. I am using sd coupling.
If I couple the protein
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