Dear Amber Users,
a short update from my site:
I managed to convert the units and set the efz value (it is set to
-0.05793, does it look reasonable?), but when I've added that in my input
file and ran the simulation, I got the following error:
| ERROR: External electric fields cannot be used when ntp is 1 (Berendsen
Barostat)!
Note, that I'm not using the Berendsen barostat.
Is there a way to run the NPT simulations? I've never run an NVT
production, and I'm a bit concerned. Is it safe for my system?
I tried to run it as an NVT simulation:
Production 303K 10ns
&cntrl
imin=0,
ntx=1, ! coordinates, but no velocities, will be read
irest=0,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=5000000,
ntt=3,
gamma_ln=1.0,
temp0=303.0,
ntpr=500,
ntwr=500,
ntwx=500,
dt=0.002,
ig=-1,
ntb=1, ! constant volume
ntp=0, ! no pressure scaling
cut=10.0,
ioutfm=1,
ntxo=2,
efz=-0.05793 ! -0.5 mV voltage
/
but it crashed at the very beginning
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = ************** EKtot = 0.0000 EPtot =
**************
BOND = 10436.7896 ANGLE = 37554.9013 DIHED =
31063.9412
1-4 NB = 10329.4923 1-4 EEL = -81697.6236 VDWAALS =
**************
EELEC = -926786.1245 EHBOND = 0.0000 RESTRAINT =
0.0000
ELECTRIC_FIELD = -23.3483
Ewald error estimate: 0.3364E-04
Do I need to minimize and equilibrate the system again prior to running a
production with applied voltage?
I would really appreciate your help!
Thanks,
Karolina
śr., 23 sie 2023 o 12:56 Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> napisał(a):
> Dear Amber users,
>
> I would like to apply an external electric field across the z-axis of my
> system, which is a membrane-bound protein.
> I searched the manual for some information, and I got a list of parameters
> which are related to electric field, such as efz, efn, frcopt, efphase, and
> effreq. But I feel a bit lost here...
>
> So, let's say I want to have a voltage of -500 eV across the z-axis (the
> membrane). Which parameters should I include in my production file?
> Also, according to the manual of Amber22, this function is not implemented
> in pmemd.CUDA - is it true?
>
> This is my standard production run:
> Production 303K 10ns
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=5000000,
> ntt=3,
> gamma_ln=1.0,
> temp0=303.0,
> ntpr=500,
> ntwr=500,
> ntwx=500,
> dt=0.002,
> ig=-1,
> ntb=2,
> ntp=2,
> cut=10.0,
> ioutfm=1,
> ntxo=2,
> /
>
> Looking forward for your help!
> Thanks,
> Karolina Mitusińska
>
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Received on Thu Aug 24 2023 - 03:00:02 PDT
