Hi Momin,
This won’t work unless you are simulating only single molecules i.e. only
unit cell with box parameters same as unit cell. Broken molecules will have
larger distances between atoms than actual bond length in a crystal
containing more than one unit cell, which will give error. So you
On Wed, Aug 1, 2018 at 7:42 AM, Nagasree Garapati <
nagasree.garap...@mail.wvu.edu> wrote:
> Thank You Dan and Lakshman
>
>
> I will try using gmx editconf and try to translate and see if I could get
> the arrangement.
>
> I am trying to create a super cell of 7x7x1 size and each unit cell has
>
Hello experts,
First, I want to mention that I am using Gromacs 2018.1.
I was wondering what the differences between pullx.xvg and gmx distance are.
"pullx.xvg" is the output of an umbrella sample mdrun.
"distance.xvg" is the output of the following command (I am comparing the
z-component
Thank you so much.
On Mon, 6 Aug 2018, 23:50 Groenhof, Gerrit, wrote:
>
> I live in iran and we don't access to Gaussian.
> You think DFTB3 (maybe)could be better choice as it's free?
>
> As I wrote earlier, that depends on whether DFTB3 provides a sufficiently
> accurate description for your
I live in iran and we don't access to Gaussian.
You think DFTB3 (maybe)could be better choice as it's free?
As I wrote earlier, that depends on whether DFTB3 provides a sufficiently
accurate description for your system. To find that out you need to either
perform a series of benchmarks, or go
Yup. Didn't even notice.
On Mon, Aug 6, 2018, 12:50 PM Justin Lemkul wrote:
>
>
> On 8/6/18 9:07 AM, Lucia Mydlova wrote:
> > Thank you very much for your helpful advice.
> >
> > I simulated polymer PMMA with two organic chromophores in NVT ensemble
> for
> > 2ns and, the same system one more
On 8/6/18 9:07 AM, Lucia Mydlova wrote:
Thank you very much for your helpful advice.
I simulated polymer PMMA with two organic chromophores in NVT ensemble for
2ns and, the same system one more time for 1.5ns
with parameters:
constraints = none
integrator = md
dt
The generally accepted protocol for simulations that end up running in
NPT is EM > relaxation NPT (possibly a series of relaxations) >
production NPT. You will almost certainly see high pressure fluctuations
right after NVT, especially given your extremely short timescales. Also,
your tau_t is
Hi,
I live in iran and we don't access to Gaussian.
You think DFTB3 (maybe)could be better choice as it's free?
Best
Sent from my iPhone
> On Aug 6, 2018, at 13:40, "Groenhof, Gerrit" wrote:
>
> Hi,
>
>
>> Is it free to use Gaussian?( as it's not free software generally)
>
> Gaussian is a
Thank you very much for your helpful advice.
I simulated polymer PMMA with two organic chromophores in NVT ensemble for
2ns and, the same system one more time for 1.5ns
with parameters:
constraints = none
integrator = md
dt = 0.001
nsteps =
Hi,
> Is it free to use Gaussian?( as it's not free software generally)
Gaussian is a commercial program, but perhaps your research group, department,
or computer center etc. have purchased it already.
If you want a free general purpose QM program, you could consider Gamess-US.
When using
Hi,
You need to compile with the QMMM-flag on
GMX_QMMM_PROGRAM = gaussian
of for older versions --with-qmmm-gaussian
After that you can use the script at to run a QM/MM simulations with any
version of the Gaussian program.
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
Best,
Gerrit
Hello GROMACS Users,
I am interested in calculating spatially resolved diffusion constants. Is
this possible? In GROMACS 2018.1, gmx msd does not seem to support dynamic
selection like gmx select.
Best,
Eric
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