[gmx-users] g_hbond

[sulatha M. S]

I did not get a warning here. I also have simulations (20ns) of
>> copolyacids where again it gave me negative life time. These runs are
>> well equilibrated with respect to energy and Rg of the polymers. The
>> system is a 20 repeat unit chain in approx. 5500 water molecules. I have
>> done simulations in which 10 units are COO- and the remaining 10 as COOH
>> along the chain. With a 10ns trajectory, the average life time of
>> H-bonds is positive.Only in the case of unionized acid I am getting a
>> negative life time.
>>
>>  Did you look at the ACF graph? It could be constant at 1 or 0.
>

Yes, the ACF decays to 0 and remains constant in all cases



>
>>
>>    Thankyou for any help,
>>
>>    Dr. M. S. Sulatha
>>    Dept. of Chemical Engineering
>>    IIT-Madras
>>    India
>>
>>
>>
>>
>>    --
>>    David van der Spoel, Ph.D., Professor of Biology
>>    Dept. of Cell & Molec. Biol., Uppsala University.
>>    Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>    spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>
>>    http://folding.bmc.uu.se
>>    --
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>>    What is the value for free energy of H-bonding.
>>
>>
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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