From: Fidan Sumbul (fidansumbul_at_gmail.com)
Date: Tue Nov 07 2017 - 02:55:40 CST
Hi Haohao,
Thank you for the comment. Yes i already checked the initial files, they are fine. And i turned off the binaryoutputs, now the job is running. We will see whether it is a problem of not using binary output or not.
Best regards,
Fidan Sumbul
> On 7 Nov 2017, at 06:27, Haohao Fu <fhh2626_at_gmail.com> wrote:
>
> Hi Fidan Sumbul,
>
> Just check your initial PDB and PSF files. If they are correct, I think at least binary restart files (binaryoutput yes, binaryrestart yes) should work.
>
> Cheers,
> Haohao
>
> 2017-11-07 1:11 GMT+08:00 Fidan Sumbul <fidansumbul_at_gmail.com>:
>> Dear NAMD users,
>>
>> I run an MD equilibration, everything seems perfect except the atom indices in .coor files.
>> When I was trying to restart a continuing simulations i saw that the coor files is not written appropriately like in the part below. Do you have any idea what could be the reason of having this problem?
>>
>> ATOM 19599 H2 TIP3W8978 -21.505 -14.565 16.296 1.00 0.00 WT8 H
>> ATOM 1959 OH2 TIP3W8984 -8.440 -9.959 303.081 1.00 0.00 WT8 O
>> ATOM 1959 H1 TIP3W8984 -7.847 -9.284 302.749 1.00 0.00 WT8 H
>> ATOM 1959 H2 TIP3W8984 -8.142 -10.120 303.976 1.00 0.00 WT8 H
>> ATOM 1959 OH2 TIP3W8988 -16.633 -0.772 259.331 1.00 0.00 WT8 O
>> ATOM 1959 H1 TIP3W8988 -16.634 -0.076 259.989 1.00 0.00 WT8 H
>> ATOM 1959 H2 TIP3W8988 -16.278 -1.534 259.789 1.00 0.00 WT8 H
>> ATOM 195 OH2 TIP3W8994 19.399 -20.651 397.430 1.00 0.00 WT8 O
>> ATOM 195 H1 TIP3W8994 18.728 -19.999 397.230 1.00 0.00 WT8 H
>> ATOM 195 H2 TIP3W8994 19.567 -20.545 398.366 1.00 0.00 WT8 H
>> ATOM 195 OH2 TIP3W9001 1.257 -1.078 402.300 1.00 0.00 WT8 O
>> ATOM 195 H1 TIP3W9001 0.470 -1.324 402.785 1.00 0.00 WT8 H
>> ATOM 195 H2 TIP3W9001 1.977 -1.255 402.906 1.00 0.00 WT8 H
>> ATOM 195 OH2 TIP3W9004 8.523 21.799 -17.381 1.00 0.00 WT8 O
>> ATOM 195 H1 TIP3W9004 9.365 22.032 -16.990 1.00 0.00 WT8 H
>>
>> …
>>
>> ATOM 19618 OH2 TIP3W9234 24.936 -0.275 349.858 1.00 0.00 WT8 O
>> ATOM 19619 H1 TIP3W9234 24.706 0.158 349.036 1.00 0.00 WT8 H
>> ATOM 1961 H2 TIP3W9234 24.350 -1.030 349.905 1.00 0.00 WT8 H
>> ATOM 1961 OH2 TIP3W9235 18.019 -13.473 360.731 1.00 0.00 WT8 O
>> ATOM 1961 H1 TIP3W9235 17.725 -14.272 360.294 1.00 0.00 WT8 H
>> ATOM 1961 H2 TIP3W9235 18.933 -13.375 360.463 1.00 0.00 WT8 H
>> ATOM 1961 OH2 TIP3W9241 23.147 6.036 116.004 1.00 0.00 WT8 O
>> ATOM 1961 H1 TIP3W9241 22.975 6.784 116.576 1.00 0.00 WT8 H
>> ATOM 19620 H2 TIP3W9241 24.010 6.214 115.629 1.00 0.00 WT8 H
>> ATOM 19621 OH2 TIP3W9250 20.174 5.935 258.046 1.00 0.00 WT8 O
>> ATOM 19622 H1 TIP3W9250 20.359 6.627 257.411 1.00 0.00 WT8 H
>>
>> Best,
>> Fidan Sumbul, PhD
>> Postdoctoral Researcher
>> U1006 INSERM
>>
>> Parc Scientifique et Technologique de Luminy
>> Bâtiment Inserm TPR2 bloc 5
>> 163 avenue de Luminy
>> 13009 Marseille
>> France
>>
>>
>
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