Hi Kungking
look for overlaps in your structures and use pmemd instead of pmemd.cuda
for debugging
On 03/09/2017 10:59 AM, kungking Hanpaibool wrote:
> Dear Amber straff
>
>
>
> I try to run MD in heating step in Amber16 and got the problem.
>
> In the first I try to heat the temperature into 298K and running finished.
>
> And the constant pressure. When I type the command, it didn’t run. It show this
>
>
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
>
>
>
>
>
> and the mdout show
>
>
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------
>
> 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
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.33
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.80
>
> |---------------------------------------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 432.82 PRESS = -802.9
>
> Etot = 48503371.9162 EKtot = 40009.1227 EPtot = 48463362.7935
>
> BOND = 911.9368 ANGLE = 2499.6931 DIHED = 4142.5033
>
> 1-4 NB = 1197.1437 1-4 EEL = 14307.5023 VDWAALS = 15832.1227
>
> EELEC = -180064.7004 EHBOND = 0.0000 RESTRAINT = 48604536.5919
>
> EAMBER (non-restraint) = -141173.7984
>
> EKCMT = 11930.2249 VIRIAL = 20549.2901 VOLUME = 497163.7231
>
> Density = 0.9323
>
> ------------------------------------------------------------------------------
>
>
>
> And then I try to change pmemd.cuda to pmemd
>
> It show like this
>
>
>
> STOP PMEMD Terminated Abnormally!
>
>
>
> And the mdout show
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------
>
> 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
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.33
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.80
>
> |---------------------------------------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 434.66 PRESS = -791.4
>
> Etot = 48503541.9934 EKtot = 40179.3009 EPtot = 48463362.6926
>
> BOND = 911.9368 ANGLE = 2499.6931 DIHED = 4142.5033
>
> 1-4 NB = 1197.1437 1-4 EEL = 14307.5023 VDWAALS = 15832.1413
>
> EELEC = -180064.8200 EHBOND = 0.0000 RESTRAINT = 48604536.5919
>
> EAMBER (non-restraint) = -141173.8994
>
> EKCMT = 12054.3531 VIRIAL = 20549.5648 VOLUME = 497163.7231
>
> Density = 0.9323
>
> Ewald error estimate: 0.2855E-04
>
> ------------------------------------------------------------------------------
>
>
>
> vlimit exceeded for step 4; vmax = 42.5727
>
>
>
> Coordinate resetting cannot be accomplished,
>
> deviation is too large
>
> iter_cnt, my_bond_idx, i and j are : 1 2411 4913 4914
>
>
>
>
>
>
>
> I also try to print every 1 step "ntpr=1" and the result show like this
>
>
> NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = NaN PRESS =515239.0
> Etot = NaN EKtot = NaN EPtot = **************
> BOND = ************** ANGLE = 736461.8217 DIHED = 15309.5865
> 1-4 NB = 14900774.0269 1-4 EEL = -2083.3537 VDWAALS = **************
> EELEC = -259199.2997 EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = **************
> EKCMT = 0.0000 VIRIAL = -4941694.8037 VOLUME = 444211.0842
> Density = 1.0435
> ------------------------------------------------------------------------------
>
>
> NSTEP = 16 TIME(PS) = 0.032 TEMP(K) = NaN PRESS =475740.7
> Etot = NaN EKtot = NaN EPtot = **************
> BOND = ************** ANGLE = 743349.7965 DIHED = 15508.2574
> 1-4 NB = 1822888.0287 1-4 EEL = -931.7176 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = **************
> EKCMT = 0.0000 VIRIAL = -4772569.5667 VOLUME = 464626.6813
> Density = 0.9976
> ------------------------------------------------------------------------------
>
>
> NSTEP = 17 TIME(PS) = 0.034 TEMP(K) = NaN PRESS =********
> Etot = NaN EKtot = NaN EPtot = **************
> BOND = ************** ANGLE = 715135.2388 DIHED = 15385.1657
> 1-4 NB = 41413.9749 1-4 EEL = -437.6827 VDWAALS = **************
> EELEC = -314929.0838 EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = **************
> EKCMT = 0.0000 VIRIAL = 2714119.2909 VOLUME = 484343.5689
> Density = 0.9570
> ------------------------------------------------------------------------------
>
>
> NSTEP = 18 TIME(PS) = 0.036 TEMP(K) = NaN PRESS =-34870.1
> Etot = NaN EKtot = NaN EPtot = **************
> BOND = ************** ANGLE = 673630.5043 DIHED = 15356.0768
> 1-4 NB = 87.5157 1-4 EEL = -213.4070 VDWAALS = **************
> EELEC = -361219.7426 EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = **************
> EKCMT = 0.0000 VIRIAL = 356214.8159 VOLUME = 473130.6767
> Density = 0.9797
> ------------------------------------------------------------------------------
>
> "5lrn_eq1.mdout" 474L, 24088C
>
> This step was seted constant pressor.
> Could you suggest me How can solve this problem?
>
>
> Best regards,
> Kungking
>
>
>
>
> ________________________________
>
>
> Dear Amber straff
>
>
>
> I try to run MD in heating step in Amber16 and got the problem.
>
> In the first I try to heat the temperature into 298K and running finished.
>
> And the constant pressure. When I type the command, it didn’t run. It show this
>
>
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
>
>
>
>
>
> and the mdout show
>
>
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------
>
> 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
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.33
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.80
>
> |---------------------------------------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 432.82 PRESS = -802.9
>
> Etot = 48503371.9162 EKtot = 40009.1227 EPtot = 48463362.7935
>
> BOND = 911.9368 ANGLE = 2499.6931 DIHED = 4142.5033
>
> 1-4 NB = 1197.1437 1-4 EEL = 14307.5023 VDWAALS = 15832.1227
>
> EELEC = -180064.7004 EHBOND = 0.0000 RESTRAINT = 48604536.5919
>
> EAMBER (non-restraint) = -141173.7984
>
> EKCMT = 11930.2249 VIRIAL = 20549.2901 VOLUME = 497163.7231
>
> Density = 0.9323
>
> ------------------------------------------------------------------------------
>
>
>
> And then I try to change pmemd.cuda to pmemd
>
> It show like this
>
>
>
> STOP PMEMD Terminated Abnormally!
>
>
>
> And the mdout show
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------
>
> 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
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.33
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.80
>
> |---------------------------------------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 434.66 PRESS = -791.4
>
> Etot = 48503541.9934 EKtot = 40179.3009 EPtot = 48463362.6926
>
> BOND = 911.9368 ANGLE = 2499.6931 DIHED = 4142.5033
>
> 1-4 NB = 1197.1437 1-4 EEL = 14307.5023 VDWAALS = 15832.1413
>
> EELEC = -180064.8200 EHBOND = 0.0000 RESTRAINT = 48604536.5919
>
> EAMBER (non-restraint) = -141173.8994
>
> EKCMT = 12054.3531 VIRIAL = 20549.5648 VOLUME = 497163.7231
>
> Density = 0.9323
>
> Ewald error estimate: 0.2855E-04
>
> ------------------------------------------------------------------------------
>
>
>
> vlimit exceeded for step 4; vmax = 42.5727
>
>
>
> Coordinate resetting cannot be accomplished,
>
> deviation is too large
>
> iter_cnt, my_bond_idx, i and j are : 1 2411 4913 4914
>
>
>
>
>
> Could you suggest me How can solve this problem?
>
>
>
> Best regards,
>
> Kungking
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Thu Mar 09 2017 - 02:30:02 PST
