AMBER Archive (2004)

Subject: Re: AMBER: water hole

From: Holly Freedman (holly_at_mercury.hec.utah.edu)
Date: Mon Apr 12 2004 - 19:39:19 CDT

Thanks Prof. Case,

Here is the prepin file. This one is for 2oxopyridine, which gave the
error message. Our simulation for 2hydroxypyridine is running, but it
also shows a channel in the water box.

    0 0 2

This is a remark line
molecule.res
MOL XYZ 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 N1 n M 3 2 1 1.540 111.208 180.000 -0.445
   5 H5 hn E 4 3 2 1.013 56.765 -0.000 0.333
   6 C1 ca M 4 3 2 1.364 177.226 0.000 0.047
   7 H1 h4 E 6 4 3 1.084 116.264 0.000 0.169
   8 C2 ca M 6 4 3 1.364 120.322 -180.000 -0.370
   9 H2 ha E 8 6 4 1.082 120.395 180.000 0.175
  10 C3 ca M 8 6 4 1.428 118.005 0.000 0.110
  11 H3 ha E 10 8 6 1.087 118.962 180.000 0.129
  12 C4 ca M 10 8 6 1.365 121.459 0.000 -0.473
  13 H4 ha E 12 10 8 1.084 122.083 180.000 0.189
  14 C5 c M 12 10 8 1.453 121.753 0.000 0.796
  15 O1 o M 14 12 10 1.228 127.162 180.000 -0.659

LOOP
   C5 N1

IMPROPER
   C5 C1 N1 H5
   C2 H1 C1 N1
   C1 C3 C2 H2
   C4 C2 C3 H3
   C5 C3 C4 H4
   C4 N1 C5 O1

DONE
STOP

-- Holly

David A. Case wrote:

>On Mon, Apr 12, 2004, Holly Freedman wrote:
>
>
>
>>We are trying to perform AMBER simulations on hydroxypyridine and
>>oxopyridine. We ran Gaussian using ESP to get the charge fitting and
>>then got an AMBER prep file and a force field modification for gaff
>>using antechamber. We added water, relaxed, thermalized to 298 and then
>>equilibrated the structure. We have been leaving the structure fixed at
>>the minimum energy structure from Gaussian. However about 70000 steps
>>into the md, we started to get messages about vlimit being exceeded and
>>also vmax = nan. Would you please have a look at my input and the
>>output meesage and give me your advice on how to fix the input?
>>Here's the input file for the md run:
>>
>>&cntrl
>> imin = 0,
>> ntx = 1, irest = 0, ibelly = 1,
>> ntpr = 100, ntwr = 100, iwrap = 1,
>> ntwx = 100, ntwe = 5000,
>> ntf = 2, ntb = 2, cut = 10,
>> nstlim = 100000, dt = .002,
>> tempi = 298, temp0 = 298, ntt = 1,
>> ntp = 1, taup = 1.0,
>> ntc = 2,
>>&end
>>Moving region
>>RES 2 826
>>END
>>END
>>
>>Here is the error message in the output file:
>>
>>NSTEP = 74200 TIME(PS) = 159.400 TEMP(K) = 420.11 PRESS = -154.6
>>Etot = -5216.0784 EKtot = 2066.2222 EPtot = -7282.3006
>>BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
>>1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1031.1950
>>EELEC = -8313.4956 EHBOND = 0.0000 RESTRAINT = 0.0000
>>EKCMT = 1040.4340 VIRIAL = 1136.4725 VOLUME = 28777.8501
>> Density = 0.8631
>>Ewald error estimate: 0.1118E-01
>>------------------------------------------------------------------------------
>>
>>vlimit exceeded for step 74238; vmax = nan
>>
>>
>
>
>I don't think it's possible to debug this just from the information you
>have, but here are some comments and things to look at:
>
>1. You are setting ntx=1, irest=0, which means that you are basically
>"starting over", and not getting any benefit from your initial equilibration
>run. Once you have done some equilibration, subsequent runs should use ntx=5,
>irest=1.
>
>2. It is possible that using the belly option is causing some problem. It is
>this that answers Carlos Simmerling's question about why you have no bond,
>angle or dihedral terms -- they are removed from the belly, and everything
>(I'm guessing) is water. The Amber 8 Users's Manual adds the following to the
>"ibelly" option description: "Note that this option does _not_ provide any
>significant speed advantage, and is maintained primarily for backwards
>compatibilty with older version of Amber. Most applications should use the
>_ntr_ varialbe instead to restrain parts of the system to stay close to some
>initial configuration."
>
>But having said this, I don't _think_ belly is causing your problem. But
>removing that option would be something to try.
>
>3. You are trying to equilibrate both the temperature and the pressure
>(volume) at the same time, which is generally a bad idea. It is certainly
>much safer to equilibrate first with ntb=1, ntp=0 to the desired final
>temperature, then switch to constant pressure (ntb=2, ntp=1). It is of
>concern that your temperature (above) is very high (420K) and the density
>is very low (0.86). The problems with the simulation probably began much
>earlier than this. Generally, it is safest to equilibrate at dt=0.001,
>and only switch to dt=0.002 after equilibration (if at all).
>
>4. Check to see if you have any atoms of type "ho" in your solute (sounds
>likely from hydroxypyridine). This hydrogen could have a zero vdW radius,
>and that in turn can lead to some bad regions of configuration space where
>that hydrogen can get too close to a negatively charged water oxygen atom.
>
>5. Consider posting your prepin file from antechamber. That way, others could
>try to do a water simulation and see if they can reproduce the problem.
>
>...good luck...dac
>
>
>

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