From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Aug 11 2009 - 08:58:27 CDT
Thanks Marcos,
I highly appreciate your help.You are right, there is no space for
luck. I am using explicit solvent and increasing equilibration time
upto 1ns.
Regards
S
On Mon, Aug 10, 2009 at 8:35 PM, Marcos Sotomayor<sotomayo_at_ks.uiuc.edu> wrote:
>
> Dear S
>
> You can easily adapt the ft.tcl script given in the tutorial and compute the
> work done on the system during the sample simulation (by integrating F times
> d). The total work done on the system is about 1922.938 kcal/mol, and NAMD
> reports a fairly similar increase in energy of about 1966.36 kcal/mol (the
> difference arising likely due to numerical errors in the integration and the
> use of a multiple time stepping algorithm). The increase in temperature is
> thus caused by the large forces applied in a very short simulation time and
> is not related at all to the system equilibration or any problem with either
> the simulation or NAMD.
>
> The whole NAMD tutorial was designed to teach how to do MD simulations and
> run sample simulations quickly in a not-so powerful computer. Therefore, and
> as explained many times in the tutorial, the sample SMD simulations in the
> tutorial are done in "unrealistic" conditions (vacuum) and at pulling speeds
> that are *very* large. If you pull more slowly, the applied forces will be
> smaller, the work done on the system will be smaller, and the temperature
> increase (due to the work done on the system) will be smaller. If you have a
> big enough system, pull slow enough, and do not use multiple time stepping,
> the temperature increase will be negligible.
>
> The previous conversation about temperature increase was related to
> artifacts arising from the use of a multiple time stepping algorithm. In the
> tutorial case, the temperature increase is mainly related to the conditions
> used.
>
> Needless to say, as pointed out in the tutorial, that if you want to do a
> proper SMD simulation you need to have an explicit solvent, an equilibrated
> system, and pull at speeds that are relevant to whatever system/process you
> are studying.
>
> Last but not least, there is no space here for luck. Its better to
> understand what is going on your simulations!
>
> Regards,
> Marcos.
>
> On Fri, 7 Aug 2009, snoze pa wrote:
>
>> Dear Namd users,
>>
>> Thank you very much for your support. I have a question related to
>> increase of temperature in SMD simulation. I was reading the past
>> conversation between Sterling, Marcos and Gianluca and observed that
>> the system temperature actually increases a lot in SMD simulation
>> compared to what Marcos statement of 20K.
>>
>> For example, in SMD tutorial provided in the NAMD website(ubiqutin
>> 3-1-pullcv, ubq_ww_pcv.log) , the initial TEMPAVG was 297.5483 which
>> increases up to TEMPAVG equal to 637.5142 at the end of 20000 step.
>> This is a huge increase in temperature. Do you think in the example
>> the system was not properly equilibrated?
>>
>> Somehow I was luck that my system temperature increases only by 10 and
>> 15 in two SMD simulation.
>>
>> Thank you
>>
>> S
>>
>
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