Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

2010-06-18 Thread David van der Spoel 

On 2010-06-18 20.22, Sikandar Mashayak wrote:

I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3).
With genbox I get .gro file with 34.04 molecules/nm^3 number density,
which will remain constant even if I do equilibration in NVT simulation
set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic
condition of water at 300K and 1 atm.

If you want to do NVT production, you still need to do an NPT 
equilbration, and extract the average density, otherwise your pressure 
will not be 1 atm in NVT.



thanks
sikandar

On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:

On 2010-06-18 18.24, Sikandar Mashayak wrote:

Hi

When a bulk SPC/E water box(.gro) is created using the command
"genbox
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic
condition of
water?

Is it 300K at 1atm?

thanks
sikandar

No. You have to equilibrate because the box is not completely full.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

2010-06-18 Thread Sikandar Mashayak 
I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3). With
genbox I get .gro file with 34.04 molecules/nm^3 number density, which will
remain constant even if I do equilibration in NVT simulation set up. So does
that 34.04 molecules/nm^3 corresponds to thermodynamic condition of water at
300K and 1 atm.

thanks
sikandar

On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
wrote:

> On 2010-06-18 18.24, Sikandar Mashayak wrote:
>
>> Hi
>>
>> When a bulk SPC/E water box(.gro) is created using the command "genbox
>> -cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of
>> water?
>>
>> Is it 300K at 1atm?
>>
>> thanks
>> sikandar
>>
>>  No. You have to equilibrate because the box is not completely full.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

2010-06-18 Thread David van der Spoel 

On 2010-06-18 18.24, Sikandar Mashayak wrote:

Hi

When a bulk SPC/E water box(.gro) is created using the command "genbox
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of
water?

Is it 300K at 1atm?

thanks
sikandar


No. You have to equilibrate because the box is not completely full.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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