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
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Received on Thu Mar 09 2017 - 02:00:03 PST
