Can it run at 1K?
Now is definitely the time to look at those step-by-step mdout and mdcrd
files.
Likely as not in mdout before it fails, you'll see something about GMAX
on some atom, and looking at that atom in the structure you'll see the
problem, maybe something as trivial as a bond poking through a ring.
Likely (short cut) it's in the neighborhood of atoms 3764 and 3755 ("I
and J" in your fail msg below).
The other common case is if you made a nonstandard residue, which could
be an ion.
Have you graphed your minimization and dynamics energies?
On 9/19/20 3:09 AM, Jisha B wrote:
> I tried the short run with 10.0 as target temperature and I got
>
> vlimit exceeded for step 0; vmax = **********
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1256 3754 3755
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> Should I repeat the minimization?
>
>
> On Sat, 19 Sep 2020 at 15:31, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Try setting ntpr and ntwx to 1 in order to get step-by-step energy and
>> structure.
>>
>> Also I'd try a short run with 10.0 target temperature to see if slower
>> warming might be possible. I believe using solute restraints during
>> warming is normal nowadays, and may be your ultimate solution, but I'd
>> also look at the demos for gradual warming cases.
>>
>> Bill
>>
>>
>> On 9/19/20 2:53 AM, Jisha B wrote:
>>> Dear all,
>>> I am dealing with a large system of protein-RNA-DNA. I have minimized the
>>> system. But when I started the heating stage where I have to increase the
>>> temperature from 0K to 100K, it is stuck at
>>>
>>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>>> using 5000.0 points per unit in tabled values
>>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>>> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>>> ---------------------------------------------------
>>> | Local SIZE OF NONBOND LIST = 101843086
>>> | TOTAL SIZE OF NONBOND LIST = 101843086
>>>
>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>>> 0.0
>>> Etot = -1363415.9230 EKtot = 0.0000 EPtot =
>>> -1363415.9230
>>> BOND = 2311.6832 ANGLE = 4410.0196 DIHED =
>>> 19869.1201
>>> 1-4 NB = 5810.6688 1-4 EEL = 39862.6725 VDWAALS =
>>> 207873.5245
>>> EELEC = -1643553.6116 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> Ewald error estimate: 0.6217E-04
>>>
>>> It has been in this stage for last one hour. My input for heating is
>>> Heating Equilibration - constant volume
>>> &cntrl
>>> imin = 0,
>>> irest = 0,
>>> ntx = 1,
>>> ntb = 1,
>>> cut = 10.0,
>>> ntr = 0,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 0.0,
>>> temp0 = 100.0,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> nstlim = 100000, dt = 0.002
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>> /
>>> When I repeated the simulation, I got the error vlimt exceeded error. How
>>> to solve this?
>>>
>> --
>> Phobrain.com
>>
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Received on Sat Sep 19 2020 - 05:30:01 PDT
