[gmx-users] Re: Density

[teklebrh at ualberta.ca]

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.

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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