Thanks alot Niel. The problem was ig. The calculations are now running ok.
Emmanuel.
On Tue, Jul 26, 2011 at 4:00 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> A couple of suggestions ....
>
> - Try using noshakemask on the entire solute.
> - Make sure ig is set to the same number for v0 and v1 (see amber11 bugfix
> 13)
>
> --Niel
> ________________________________________
> From: Emmanuel Baribefe Naziga [baribefe.gmail.com]
> Sent: Tuesday, July 26, 2011 12:11 PM
> To: AMBER Mailing List
> Subject: [AMBER] vdW issues during TI
>
> Dear all,
>
> I am having some trouble with TI calculation and I'm hoping to get some
> pointers on how to solve this problem.
>
> What I am trying to do is to basically mutate a sugar to a hydroxyl group.
> The issue arises in the van der Waals step using softcore potentials (step
> 2). I can minimize, heat, equilibrate and run production calculations for
> the charging steps (steps1 & 3). My input files look like this:
>
> v0:
>
> &cntrl
> imin = 0, ntx = 1, irest = 0,
> ntpr = 1 , ntwr = 1000, ntwx = 1,
> ntf = 1, ntc = 2, ntr =1, nmropt = 1,
> ntb = 1, cut = 9.0, ig = -1,
> nstlim = 50000, dt = 0.001,
> ntt = 3, gamma_ln = 5,
> icfe=1, clambda = 0.1,
> ifsc=1,
> crgmask=':4.C1
> ,H1,O5,C5,H5,C6,H61,H62,O6,H6O,C4,H4,O4,H4O,C3,H3,O3,H3O,C2,H2,O2,H2O',
> scmask=':4.C1
> ,H1,O5,C5,H5,C6,H61,H62,O6,H6O,C4,H4,O4,H4O,C3,H3,O3,H3O,C2,H2,O2,H2O',
> &end
> &wt
> TYPE='TEMP0', istep1=0, istep2=25000, value1=5.0, value2=300.0,
> /
> &wt
> TYPE='TEMP0', istep1=25001, istep2=50000, value1=300.0, value2=300.0,
> /
> &wt
> TYPE='END',
> /
> Keep nucleoside fixed with weak restraints
> 1.0
> RES 1 7
> END
> END
>
>
> v1:
>
> temperature equilibration
> &cntrl
> imin = 0, ntx = 1, irest = 0,
> ntpr = 1 , ntwr = 1000, ntwx = 1,
> ntf = 1, ntc = 2, ntr = 1, nmropt = 1,
> ntb = 1, cut = 9.0, ig = -1,
> nstlim = 50000, dt = 0.001,
> ntt = 3, gamma_ln = 5,
> icfe=1, clambda = 0.1,
> ifsc=1,
> crgmask=':4.HOD',
> scmask=':4.HOD,
> &end
> &wt
> TYPE='TEMP0', istep1=0, istep2=25000, value1=5.0, value2=300.0,
> /
> &wt
> TYPE='TEMP0', istep1=25001, istep2=50000, value1=300.0, value2=300.0,
> /
> &wt
> TYPE='END',
> /
> Keep nucleoside fixed with weak restraints
> 1.0
> RES 1 7
> END
> END
>
> I keep getting vlimit errors. I have read several messages on the list
> about
> this, tried different clambda and also removed all restraints but the
> error persists. Minimization runs without any issues. Also when I use dt =
> 0.0005 it seems to run (I have done about 500ps, although the temperature
> of
> v1 system remains ~ 600K which I have seen other people mention in the list
> archives). Using a restart from the dt = 0.0005 calculation does not solve
> the problem.
>
> When I examine the structures of the calculations that crash with this
> vlimit/SHAKE errors I find that strangely it sometimes does not occur due
> to
> the residue that is been changed.
>
> I created my initial structures from a glycosylated peptide that has been
> equilibrated by normal MD. To make the second (mutated) structure with the
> hydroxyl instead of the sugar I manually deleted the atoms corresponding to
> the sugar from a pdb file (except the glycosidic oxygen) and reloaded the
> pdb in xleap to add the hydrogen atom. There is a net charge on the peptide
> during the TI transformations but the only way I can see to have a neutral
> system is to mutate whole residues which has the same vlimit errors when I
> try.
>
> I am using GLYCAM force field for the sugar and standard amber SCEE/SCNB
> but I would think if this was the issue it might be more important in steps
> 1 and 3.
>
> Any ideas on how to tackle this is very welcome.
>
> Thanks,
>
> Emmanuel
>
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
> v0 output before crashing
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> NSTEP = 697 TIME(PS) = 498.894 TEMP(K) = 319.49 PRESS =
> 839.1
> Etot = -21886.5090 EKtot = 5835.0153 EPtot =
> -27721.5243
> BOND = 314.7526 ANGLE = 361.4444 DIHED =
> 73.3269
> 1-4 NB = 43.7350 1-4 EEL = 243.7492 VDWAALS =
> 4405.6716
> EELEC = -33164.2039 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> DV/DL = 7179.5437
> EKCMT = 3160.1045 VIRIAL = 1458.3109 VOLUME =
> 93927.6476
> Density =
> 0.9755
> Ewald error estimate: 0.2712E-04
>
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 22 atoms, TEMP(K) =
> 495.20
> SC_BOND= 15.5740 SC_ANGLE= 32.4067 SC_DIHED =
> 5.7785
> SC_14NB= 5.9273 SC_14EEL= 0.0000 SC_EKIN =
> 27.0614
> SC_VDW = -1.4267 SC_EEL = 0.0000 SC_DERIV=
> -7.7901
>
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 697; vmax = 37.2853
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 5 28 32 33
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
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Received on Tue Jul 26 2011 - 17:30:03 PDT
