From: Jiann George Pazhamalil (jgpaz1_at_student.monash.edu)
Date: Mon Jan 13 2014 - 21:37:41 CST
Thank you for your responses,
The POPC membrane was made through charmmgui and then converted accordingly
to work in the lipid11 amber force field. I am attempting to reduce the
number of steps in the NAMD simulation and seeing if that would alter the
patch grid problem. From the logout files it is visible that the system is
shrinking at a high rate.
I thought this could be due to the surfacetenstiontarget parameter as there
are discrepancies between the units used in amber and namd. In the lipid11
Amber the units were dyn/Angstrom (the value I found and am using) and namd
specifies it as dyn/cm but converting 17 to 17000000 doesn't seem right.
>From the other mailing lists everyone seems to use a value closer to 20. Is
this parameter applying pressure from outside or from within the system?
I was hoping if anyone has encountered such a simulation would explain how
they went about it?
Thanks in advance,
On 8 January 2014 10:33, Jeffrey Potoff <jpotoffx_at_gmail.com> wrote:
> On 1/7/2014 6:33 PM, Jiann George Pazhamalil wrote:
>> Dear NAMD users,
>> I am a student and extremely new at this process and I am trying to run a
>> protein and membrane simulation where I am receiving the error "FATAL
>> ERROR: Periodic cell has become too small for original patch grid!" I am
>> aware that this is a common problem and I have been looking at the archives
>> however increasing the margin or restarting the run is not helpful and I am
>> still receiving this error and with a membrane, I can't switch off
>> flexiblecell. Energy minimization and equilibration is running fine but the
>> problem is with the MD run which is unique from the previous problems seen
>> on the list. I am a little unsure about the surfaceTensionTarget value I am
>> using. I have a POPC bilayer and I'm using 17 dyn/cm, could that possibly
>> be the reason of the error?
>> With a membrane simulation, there many things that can go wrong that
> will result in "patch grid" error, such as
> 1. Not enough water in the system (density is too low).
> 2. Initial membrane structure is far from equilibrium.
> 3. Poor lipid model. Older lipid force fields had the tendency to
> "condense" when used in constant pressure simulations.
> Some solutions:
> 1. Use a one of the modern lipid force fields, like CHARMM 36, which does
> not require the application of a surface tension to produce the correct
> area per lipid.
> 2. Equilibrate for ~2-4 ns using NVT, then switch to NPT.
> 3. Use an anisotropic pressure move. In NAMD this is done by setting
> "useconstantratio" to "yes".
> 4. Make sure your initial configuration is reasonable. CHARMMGUI is
> pretty good for the generation of membrane structures.
> 5. If all else fails, try using a smaller timestep (0.5-1ns) for 0.1-1 ns
> to get the system to calm down.
> 6. Set your DCD and restart output to something small, say 100 steps and
> run a short simulation ( < 10,000 steps). Sometimes you can get NAMD to
> drop a restart file that you can bootstrap off to get a stable simulation
> Jeffrey J. Potoff jpotoff_at_wayne.edu
> Associate Professor and Director of Early Engineering Programs
> Department of Chemical Engineering and Materials Science
> Wayne State University 5050 Anthony Wayne Dr
> Detroit, MI 48202
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