From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Sat Feb 04 2017 - 06:11:52 CST
Hi,
Thank you for your helpful comments.
Regards,
Farideh
On Sat, Feb 4, 2017 at 3:30 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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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