Re: AW: High pressure calculations

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Feb 04 2017 - 06:00:53 CST

At any event, the code is not parameterized for high pressures. Don't
forget.
fp

On Sat, Feb 4, 2017 at 12:54 PM, Andrey KALINICHEV <
kalinich_at_subatech.in2p3.fr> wrote:

> I would also recommend to look at the pressure scale. For most practical
> purposes, the difference between 15 bar, 1 bar, and 0 bar is negligible,
> and may not be visible on the pressure scale of your plot.
>
> Andrey
>
>
> Le 2017-02-04 à 12:33, Norman Geist a écrit :
>
>> From the NAMDPlot plugin of VMD, export to Xmgrace and zoom the graph.
>> You will most probably notice that it is not zero, but your desired
>> target pressure.
>>
>>
>>
>> Norman Geist
>>
>>
>>
>> *Von:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *faride badalkhani
>> *Gesendet:* Freitag, 3. Februar 2017 20:24
>> *An:* Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
>> *Cc:* namd-l_at_ks.uiuc.edu
>> *Betreff:* Re: namd-l: High pressure calculations
>>
>>
>>
>> Hi,
>>
>> As you said I used the constant pressure conditions and I did not get
>> any error so far. (I am running the simulation for 10 ns). The log file
>> shows the average pressure ~15 bar, but when I plot the average pressure
>> using NAMD plot it is zero line. What do you think is wrong with the
>> system set up?
>>
>> Regards,
>>
>> Farideh
>>
>>
>>
>> On Fri, Feb 3, 2017 at 8:45 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
>> <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
>>
>> The easiest way I can think of is to just use constant pressure
>> conditions until the volume equilibrates. Is there a reason this
>> wouldn't work in your case?
>>
>> -Josh
>>
>>
>> On 02/03/2017 09:15 AM, faride badalkhani wrote:
>> Dear NAMD users,
>>
>> I want to perform simulations in high pressure (~15 bar). How can I
>> find that I have reached the desired pressure?
>>
>> Regards,
>> F.
>>
>>
>>
>>
>

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