Re: namd2_ti.pl Error: Modification of non-creatable array value attempted

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jun 04 2018 - 08:14:11 CDT

That script hasn't been very actively supported for quite some time. In
fact it is completely incompatible with NAMD versions after 2.11 (maybe
2.10?). Nonetheless, you appear to be using the older version so I suppose
it could still work.

TI is not a particularly challenging algorithm - you may have to write your
own script or even do the calculation by hand.

HTH,
BKR

On Sun, Jun 3, 2018 at 12:34 PM, Kooshul S. Jhaveri <
Kooshul.S.Jhaveri.18_at_dartmouth.edu> wrote:

> Hello,
>
> When I run namd2_ti.pl on my ti.out file, I keep getting the following
> error:
>
> *"Reading files: .Modification of non-creatable array value attempted,
> subscript -998 at ./namd2_ti.pl <http://namd2_ti.pl> line 102, <FILE> line
> 19063.”*
>
> Does anyone know how to fix this? My ti.out file looks like this (note
> there are no PME values):
>
> # STEP Elec_dU/dl Elec_avg vdW_dU/dl vdw_avg
> Elec_dU/dl Elec_avg vdW_dU/dl vdw_avg PME_dU/dl
> PME_avg
> # <---------------------PARTITION
> 1------------------------> <---------------------PARTITION
> 2--------------------->
> #NEW TI WINDOW: LAMBDA 0
> #PARTITION 1 VDW LAMBDA 0
> #PARTITION 1 ELEC LAMBDA 0
> #PARTITION 2 VDW LAMBDA 1
> #PARTITION 2 ELEC LAMBDA 0
>
> TI 1000 -70.5918 -70.5918 -16.0580 -16.0580
> -69.6079 -69.6079 29.3107 29.3107
> TI 1005 -70.1625 -70.2340 -15.6513 -15.7191
> -69.1089 -69.1921 22.0684 23.2755
> TI 1010 -68.8360 -69.5986 -14.3221 -15.0841
> -67.6407 -68.4869 3.6763 14.3668
> TI 1015 -68.3788 -69.2174 -13.3770 -14.5506
> -67.3241 -68.1235 -4.9374 8.3342
> TI 1020 -69.6186 -69.3129 -13.3637 -14.2680
> -68.9055 -68.3097 -3.2774 5.5695
> TI 1025 -71.3458 -69.7039 -13.9691 -14.2105
> -70.8649 -68.8011 5.5993 5.5753
> TI 1030 -71.7596 -70.0354 -14.5065 -14.2583
> -71.3296 -69.2089 13.9475 6.9256
> TI 1035 -70.8094 -70.1429 -14.5032 -14.2923
> -69.9292 -69.3090 14.2819 7.9473
> TI 1040 -69.3715 -70.0488 -14.2063 -14.2818
> -67.8435 -69.1302 12.0808 8.4514
> TI 1045 -69.1034 -69.9461 -14.1183 -14.2640
> -66.7837 -68.8752 11.0889 8.7381
> TI 1050 -69.7075 -69.9227 -14.2935 -14.2669
> -67.4571 -68.7361 11.8588 9.0441
> TI 1055 -71.0277 -70.0214 -14.3490 -14.2742
> -68.8702 -68.7481 16.9876 9.7533
>
>
>
> Thanks,
> Kooshul
>
>
>

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