[gmx-users] Re: Density

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> Thank you Justine
> 
> I have another question. I run my simulation for 5ns and when i just 
> check the density of my solvent, the density did not look right. I used 
> the N-H and P-R for the thermostat and barostat. Both shows the correct 
> temperature and pressure (300K and 1bar). when I use the g_density to 
> check only the density of my solvent (in this case Toluene), it shows 
> 0.933g/ml, but the actual density according to literature is 0.866g/ml. 
> I have no idea what the problem is.
> 

Well, the barostat is not the only factor that will influence your results.  The 
rest of the .mdp file is quite important as well.  Have the parameters you are 
using been validated and optimized such that they should reproduce the actual 
experimental density of toluene?  Simulated solvent and experimental solvent are 
often not the same.

-Justin

> Can you please give me some suggestions.
> 
> 
> Robel
> 
> 
> Quoting "Justin A.  Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> teklebrh at ualberta.ca wrote:
>>> Dear Gromacs users,
>>>
>>> I am using gromacs 3.3.3 for my simulation.
>>>
>>> I run my project for 5ns and want to extend to 10 ns. Can any body 
>>> tell me if this is the right way to do.
>>>
>>> tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr 
>>> -extend timetoextend
>>>
>>
>> Being that you've copied the entry from here:
>>
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>> ...I would guess that it's correct :)
>>
>>> The previous.tpr means for the 5ns MD run.
>>> The next.tpr is for the 10ns.
>>>
>>> what does the -extend means?
>>>
>>
>> Per tpbconv -h:
>>
>> "Extend runtime by this amount (ps)"
>>
>> -Justin
>>
>>> what does timetoextend means ( in my case is timetoextend is 5ns)
>>>
>>> Please give me some suggestions.
>>>
>>> Rob
>>>
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================