Re: [gmx-users] ACETONITRILE with CHARM ff

2017-07-13 Thread Justin Lemkul 



On 7/12/17 8:56 AM, Sonia Milena Aguilera Segura wrote:





Message: 3
Date: Tue, 11 Jul 2017 12:57:05 -0400
From: Justin Lemkul 

Moreover, I observed that this time I got lower values for P during the NPT
equilibration, but still is too far from 1 bar.  I really don't understand
why for the NVT simulation I get a T around 298, but as soon as I turn on
the pcoupl, the T rises to 300-301 K and the P gets average values of 7
and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of
the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7
bar. Considering the parameters I am using, is there anything I can change
to make the P coupling better? I am running a 3 nm box with 308 molecules.
This is the full mdp file:



http://www.gromacs.org/Documentation/Terminology/Pressure

Your box is very small and will be subject to large fluctuations.


Dear Justin,

I increased the size of the simulation box to 4 nm. Indeed, the values of 
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T 
keeps being overestimated (302 K). During NVT I got the right value, so I 
decided to run the 200 ns NPT equilibration with Berendsen barostat instead of 
P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. 
Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the 
-e option because it gives me the error Could not find energy term named 
'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect 
stored values for it?. But I am using -t ). Despite I got low pressure averages 
around 0.5 bar, the temperature raised again to 301-302. This happens very 
early in the simulation, which seems to indicate that for sd 
integrator/thermostat and P-R barostat there is something going on. I am 
getting practically the same density in between simulation, so I guess I can 
say t

ha

  t in term of P, the system has been equilibrated. However, what can I do to 
get the right T for this system? If I was able to get the right T with 
Berendsen barostat, I don't understand what's wrong when I change to P-R.



Sounds buggy.  What version of GROMACS are you using?  There were temperature 
issues with the Langevin integrator in previous versions, but those should have 
been long since solved.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] ACETONITRILE with CHARM ff

2017-07-12 Thread Sonia Milena Aguilera Segura 


> 
> Message: 3
> Date: Tue, 11 Jul 2017 12:57:05 -0400
> From: Justin Lemkul 
> > Moreover, I observed that this time I got lower values for P during the NPT
> > equilibration, but still is too far from 1 bar.  I really don't understand
> > why for the NVT simulation I get a T around 298, but as soon as I turn on
> > the pcoupl, the T rises to 300-301 K and the P gets average values of 7
> > and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of
> > the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7
> > bar. Considering the parameters I am using, is there anything I can change
> > to make the P coupling better? I am running a 3 nm box with 308 molecules.
> > This is the full mdp file:
> > 
> 
> http://www.gromacs.org/Documentation/Terminology/Pressure
> 
> Your box is very small and will be subject to large fluctuations.

Dear Justin, 

I increased the size of the simulation box to 4 nm. Indeed, the values of 
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T 
keeps being overestimated (302 K). During NVT I got the right value, so I 
decided to run the 200 ns NPT equilibration with Berendsen barostat instead of 
P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. 
Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the 
-e option because it gives me the error Could not find energy term named 
'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect 
stored values for it?. But I am using -t ). Despite I got low pressure averages 
around 0.5 bar, the temperature raised again to 301-302. This happens very 
early in the simulation, which seems to indicate that for sd 
integrator/thermostat and P-R barostat there is something going on. I am 
getting practically the same density in between simulation, so I guess I can 
say tha
 t in term of P, the system has been equilibrated. However, what can I do to 
get the right T for this system? If I was able to get the right T with 
Berendsen barostat, I don't understand what's wrong when I change to P-R. 

Thank you in advance, 

Sonia Aguilera 
PhD student
ENSCM

> 
> -Justin
> 
> > ; Run control
> > integrator   = sd   ; Langevin dynamics
> > tinit= 0
> > dt   = 0.0005
> > nsteps   = 200   ; 1 ns
> > nstcomm  = 100
> > ;energygrps  = non-Water
> > ; Neighborsearching and short-range nonbonded interactions
> > cutoff-scheme= verlet
> > nstlist  = 20
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.2
> > ; Electrostatics
> > coulombtype  = PME
> > rcoulomb = 1.2
> > ; van der Waals
> > vdwtype  = cutoff
> > vdw-modifier = force-switch
> > rvdw-switch  = 1.0
> > rvdw = 1.2
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr  = no
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing   = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme_order= 6
> > ewald_rtol   = 1e-06
> > epsilon_surface  = 0
> > ; Temperature coupling
> > ; tcoupl is implicitly handled by the sd integrator
> > tc_grps  = system
> > tau_t= 1.0
> > ref_t= 298.15
> > ; Pressure coupling is on for NPT
> > Pcoupl   = Parrinello-Rahman
> > tau_p= 1.0
> > compressibility  = 4.5e-05
> > ref_p= 1.0
> > ; Do not generate velocities
> > gen_vel  = no
> > ; options for bonds
> > constraints  = none  ; we only have C-H bonds here
> > ; Type of constraint algorithm
> > constraint-algorithm = lincs
> > ; Constrain the starting configuration
> > ; since we are continuing from NPT
> > continuation = yes
> > ; Highest order in the expansion of the constraint coupling matrix
> > lincs-order  = 12
> > 
> > 
> > Thank you very much,
> > 
> > Sonia Aguilera
> > PhD student
> > ENSCM
> >> ; Run control
> >> integrator   = sd   ; Langevin dynamics
> >> tinit= 0
> >> dt   = 0.0005
> >> nsteps   = 4000   ; 20 ns
> >> nstcomm  = 100
> >> ; Neighborsearching and short-range nonbonded interactions
> >> cutoff-scheme= verlet
> >> nstlist  = 20
> >> ns_type  = grid
> >> pbc  = xyz
> >> rlist= 1.2
> >> ; Electrostatics
> >> coulombtype  = PME
> >> rcoulomb = 1.2
> >> ; van der Waals
> >> vdwtype  = cutoff
> >> vdw-modifier = potential-switch
> >> rvdw-switch  = 1.0
> >> rvdw = 1.2
> >> ;