I am experiencing some other problem, it seems that the OPC water simulation works as intended though a box with a capped hexapeptide and a Cl- ion does not.
I have run 6 short simulations 3 with only water (OPC, SPCE and TIP3P) as well as 3 with the same water models as well as a hexapeptide and a chloride ion (FF14SP-SPCE, FF14SB-TIP3P and FF19SB-OPC).
All systems with only water equilibrates nicely inside the timeframe. The pressure equilibration of OPC water is finished faster then the SPCE and TIP3P models and all simulation produce usable plots with the “process_m*.perl” scripts. Everything looks fine.
The FF19SB-OPC system does NOT behave as intended. I can keep hammering this system with higher pressure and shorter taup though looking at the simulation, it seems like I am trying to equilibrate a block of ice with air trapped inside: https://gifyu.com/image/865p (Do note that I have NOT autoimaged with CPPTRAJ, the restricted motion of the water prevents changing the shape).
Running only OPC water works just fine, so it seems that it is the FF19SB part which does not work as intended. For some reason, the entire system appears to be suffering from some motion restriction though I have implemented none. I have tried to see if the manual contained any information regarding particular options for input files or similar but did not find anything.
I used the same input for all simulations:
Energy minimization, 5000 steps SD then 5000 CG
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntb=1,
cut=9.0,
/
125 ps to constant T
&cntrl
ig =-1,
imin = 0,
iwrap = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 9.0,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 293.15,
ntt = 3,
gamma_ln = 1.0,
nstlim = 62500, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 2000
/
Constant T, pressure eq: 500 ps MD
&cntrl
ig =-1,
imin = 0,
iwrap = 0,
irest = 1,
ntx = 5,
ntb = 2,
pres0 = 1,
ntp = 1,
barostat = 1,
taup = 2.0,
cut = 9.0,
ntc = 2,
ntf = 2,
tempi = 293.15,
temp0 = 293.15,
ntt = 3,
gamma_ln = 1.0,
nstlim = 250000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 2000
/
All the intended output files are produced and seemingly (except for the restricted motion) looks normal and reads just fine in cpptraj and vmd.
Any ideas regarding what I am doing wrong?
Best regards
// Gustaf
> On 22 Oct 2020, at 15:06, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> Dave - no I haven't tried that during equilibration, since tighter coupling
> fixes it I just made it part of our equilibration protocol long ago and
> moved on. I'll try that since I have a sample setup with a bubble and see
> if it works better.
> carlos
>
> On Thu, Oct 22, 2020 at 8:48 AM David A Case <david.case.rutgers.edu> wrote:
>
>> On Wed, Oct 21, 2020, Carlos Simmerling wrote:
>>
>>> what is your pressure coupling constant? I often get vacuum bubbles unless
>>> I include a step in my equilibration with tight coupling, taup around 0.1
>>> or smaller.
>>
>> Carlos: have you ever tried barostat=2? It would be interesting to know
>> if that makes a difference. Also, what is your starting density? If
>> you use a closeness parameter of 0.7--0.8 (in solvateBox or solvateOct),
>> you'll get a higher starting density, which might(?) reduce the tendency
>> to get bubbles.
>>
>> ....dac
>>
>>
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Received on Fri Oct 23 2020 - 02:30:02 PDT
