O'right, it seems that I did everything correctly.
Thank you for your help! :)
2015-09-05 14:30 GMT+01:00 Dawid das :
> Yes, that is right Justin. But I still need:
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein non-Protein ; two coupli
On 9/5/15 9:30 AM, Dawid das wrote:
Yes, that is right Justin. But I still need:
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in
Yes, that is right Justin. But I still need:
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300
On 9/5/15 5:48 AM, Dawid das wrote:
I struggle to properly define my *mdp file. I have following keywords and
their values:
;Simulated annealing is on
annealing = single
annealing-npoints = 30 30
annealing-time = 0.0 0.002 5.0 5.002 10.0 10.002 15.0 15.002 20.0
20.002 25.0 25.
Hi,
Not sure what the problem is, but you should start with a simple one step
annealing of one group. Get that right, then get complex.
Mark
On Sat, Sep 5, 2015 at 11:49 AM Dawid das wrote:
> I struggle to properly define my *mdp file. I have following keywords and
> their values:
>
> ;Simulat
I struggle to properly define my *mdp file. I have following keywords and
their values:
;Simulated annealing is on
annealing = single
annealing-npoints = 30 30
annealing-time = 0.0 0.002 5.0 5.002 10.0 10.002 15.0 15.002 20.0
20.002 25.0 25.002 30.0 30.002 35.0 35.002 40.0 40.002
2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban :
> However, your simulation schedule makes little sense physically .
>
What do you mean by that? I just want to heat up my system gently before
equilibration phase.
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annealing-time: 0.000 0.001 5.000 5.001 10.000 10.001 15.000
annealing-temp: 0 20 20 40 40
60 60
However, your simulation schedule makes little sense physically .
Remember that what you change here of the thermostat's reference
temperature, n
On 9/4/15 1:04 PM, Dawid das wrote:
Dear Gromacs Experts,
Is it possible to do following heating of my system:
increase reference temperature by 20 K every 5 ps of simulation in one run
until I reach 300 K?
http://manual.gromacs.org/online/mdp_opt.html#sa
-Justin
--
==
Dear Gromacs Experts,
Is it possible to do following heating of my system:
increase reference temperature by 20 K every 5 ps of simulation in one run
until I reach 300 K?
According to what I found in one of papers, it is possible to do with NAMD.
Best wishes,
Dawid Grabarek
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Gromacs Users ma
On 2/20/15 6:11 AM, Rahul Chatterjee wrote:
Hello,
I have been trying to simulate a fluid over a heated substrate. I either
need to freeze or restrain the particles on the substrate in order to make
them behave as rigid wall.However, this would not allow me to have a
thermostat declared for the
Hello,
I have been trying to simulate a fluid over a heated substrate. I either
need to freeze or restrain the particles on the substrate in order to make
them behave as rigid wall.However, this would not allow me to have a
thermostat declared for the wall particles and coupling them to thermostats
Hi Kiana,
Simulated annealing will take your system temperature distribution to the
target temperature. So, I always start at the starting point.
Hi Vitaly,
Heating slowly (over many ns) from 0K-xK seems to be an important step in
crystal simulations performed by other members in my lab...in fact,
Is that really so fulminant? For a gram of water it takes 1.2 kJ. Over 100
ps that requires only a modest laser :)
Tsjerk
On Wed, Dec 4, 2013 at 12:27 PM, Dr. Vitaly Chaban wrote:
> Honestly, I see no sense in heating from from 0 to 300 K. As long as
> the system is in the solid state, it is
Honestly, I see no sense in heating from from 0 to 300 K. As long as
the system is in the solid state, it is probably not informative to
handle it. Thus heating, if any, might start from the freezing point.
Moreover, heating from 0 to 300 K over 100 ps is so fulminant that it
does not correspond to
Hi Kiana,
I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5
(starting temp). 5 K is as good as starting at 0 K for my systems. Hope
that helps.
Regards,
On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam wrote:
> Dear Jastin
>
> Thanks very much for your reply, when I he
Dear Jastin
Thanks very much for your reply, when I heat system from 0 to 300 K with
simulated annealing, ref_t =300 is correct?
Best Regards
On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul wrote:
On 12/3/13 2:17 AM, kiana moghaddam wrote:
> Dear GMX Users
>
> I want to run NVT equil
It is an interesting question, because how does one generate velocities at
> 0 K?
>
Random sampling from a Maxwellian distribution with mean zero and zero
width :) At the end of the first step all velocities will be scaled to
zero. That shouldn't be very unstable.
Cheers,
Tsjerk
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On 12/3/13 2:17 AM, kiana moghaddam wrote:
Dear GMX Users
I want to run NVT equilibration and NPT equilibration (after NVT) and want to
increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have
some questions about this process:
when I use simulated annealing in NVT as foll
Dear GMX Users
I want to run NVT equilibration and NPT equilibration (after NVT) and want to
increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have
some questions about this process:
when I use simulated annealing in NVT as following
annealing_time = 0 15 30 45
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