I did run a set of TI calculations and I have got 10 windows ( clambda varies from 0 to 1 , in increments of 0.1)
Amber tutorial does not explain to how to analyze the output file.
Here Is a small snapshot of output I have obtained at clambda 0.2
| Running AMBER/MPI version on 12 MPI task
--------------------------------------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.89
|---------------------------------------------------
DOF for the SC part 1 of the system: 15
SHAKE constraints in the SC region: 3
| TI region 1
NSTEP = 100 TIME(PS) = 20.200 TEMP(K) = 290.38 PRESS = -399.0
Etot = -108450.2812 EKtot = 25965.5439 EPtot = -134415.8251
BOND = 832.3288 ANGLE = 2261.1386 DIHED = 3619.6989
1-4 NB = 1082.4932 1-4 EEL = 13357.7682 VDWAALS = 16246.6326
EELEC = -171815.8853 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 11336.6260 VIRIAL = 15272.6118 VOLUME = 456922.8451
Density = 0.9772
DV/DL = 5.7164
Ewald error estimate: 0.6441E-04
------------------------------------------------------------------------------
Softcore part of the system: 6 atoms, TEMP(K) = 143.60
SC_Etot= -21.3627 SC_EKtot= 2.1403 SC_EPtot = -23.5030
SC_BOND= 0.0410 SC_ANGLE= 1.6689 SC_DIHED = 0.0000
SC_14NB= -0.0600 SC_14EEL= -25.1529 SC_VDW = 0.0000
SC_EEL = 0.0000
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.2987 SC_VDW_DER= -3.0336 SC_DERIV = -3.3323
------------------------------------------------------------------------------
| TI region 2
NSTEP = 100 TIME(PS) = 20.200 TEMP(K) = 290.40 PRESS = -399.0
Etot = -108452.4214 EKtot = 25963.4036 EPtot = -134415.8251
BOND = 832.3288 ANGLE = 2261.1386 DIHED = 3619.6989
1-4 NB = 1082.4932 1-4 EEL = 13357.7682 VDWAALS = 16246.6326
EELEC = -171815.8853 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 11336.6260 VIRIAL = 15272.6118 VOLUME = 456922.8451
Density = 0.9770
DV/DL = 5.7164
Ewald error estimate: 0.6441E-04
------------------------------------------------------------------------------
| TI region 1
NSTEP = 200 TIME(PS) = 20.400 TEMP(K) = 291.65 PRESS = -210.7
Etot = -107938.2534 EKtot = 26079.5430 EPtot = -134017.7964
BOND = 871.5472 ANGLE = 2320.0526 DIHED = 3617.7781
1-4 NB = 1079.9607 1-4 EEL = 13285.4803 VDWAALS = 16403.9814
EELEC = -171596.5966 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 11431.1876 VIRIAL = 13505.4824 VOLUME = 456060.0649
Density = 0.9790
DV/DL = 3.5468
Ewald error estimate: 0.5479E-04
------------------------------------------------------------------------------
Softcore part of the system: 6 atoms, TEMP(K) = 351.65
SC_Etot= -16.7666 SC_EKtot= 5.2410 SC_EPtot = -22.0077
SC_BOND= 0.5772 SC_ANGLE= 2.6107 SC_DIHED = 0.0000
SC_14NB= -0.0593 SC_14EEL= -25.1363 SC_VDW = 0.0000
SC_EEL = 0.0000
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 0.0252 SC_VDW_DER= -6.1032 SC_DERIV = -6.0780
------------------------------------------------------------------------------
| TI region 2
NSTEP = 200 TIME(PS) = 20.400 TEMP(K) = 291.64 PRESS = -210.7
Etot = -107943.4944 EKtot = 26074.3020 EPtot = -134017.7964
BOND = 871.5472 ANGLE = 2320.0526 DIHED = 3617.7781
1-4 NB = 1079.9607 1-4 EEL = 13285.4803 VDWAALS = 16403.9814
EELEC = -171596.5966 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 11431.1876 VIRIAL = 13505.4824 VOLUME = 456060.0649
Density = 0.9789
DV/DL = 3.5468
Ewald error estimate: 0.5479E-04
------------------------------------------------------------------------------
It goes on till 30000 steps and then there is a header called SUMMARY:
After summary I have a long list of numbers:-
11.1330
11.2170
11.2328
11.1343
10.9781
10.8268
10.7903
10.9089
11.1407
11.3951
11.6348
11.8611
12.0684
12.2892
12.5056
12.7248
13.0684
13.4920
13.9335
14.2562
14.3702
14.3342
14.1977
14.0142
13.8460
13.7240
13.7383
13.8980
14.1537
14.4052
14.5162
14.4927
14.3774
14.1412
13.8458
13.6290
13.5012
13.4974
13.6041
13.7142
13.7007
13.6078
13.4240
13.1314
12.9326
12.8762
12.8853
12.8641
12.8825
12.6830
12.1080
11.0983
9.4797
7.4482
5.6205
4.7567
5.0867
6.5812
8.5878
10.6210
12.2217
13.1416
13.4274
Then it says end of dv/dl summary.
SO should I be writing a script to bin out these numbers for further analyses?
Thanks
From: Ross Walker<mailto:ross.rosswalker.co.uk>
Sent: Thursday, October 24, 2019 8:56 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] TI on gpus
Hi Debarati,
TI is supported by pmemd.cuda as of Amber 18. Please see the following for the list of GPU accelerated features:
http://ambermd.org/GPUFeatures.php <
http://ambermd.org/GPUFeatures.php>
and
Tai-Sung LeeDavid S. CeruttiDan MermelsteinCharles LinScott LeGrandTimothy J. GieseAdrian RoitbergDavid A. CaseRoss C. Walker*Darrin M. York*, "
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features", J. Chem. Inf. Model.2018,58,10,2043-2050
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00462 <
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00462> /
https://doi.org/10.1021/acs.jcim.8b00462 <
https://doi.org/10.1021/acs.jcim.8b00462>
All the best
Ross
> On Oct 24, 2019, at 1:45 PM, Debarati DasGupta <debarati_dasgupta.hotmail.com> wrote:
>
> Can GPUs be used for production runs using various clambda values in Thermodynamic Integration or is it just sander.MPI /pmemd.MPI…
> Pmemd.cuda cannot handle the TI runs asof now right?
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
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Received on Fri Oct 25 2019 - 06:30:05 PDT
