[gmx-users] Re: How to control the density

[teklebrh at ualberta.ca]

Dear Justin,

> To use pdb2gmx, you need an .rtp entry.  For something like 
 > united-atom n-heptane, this should be a relatively easy exercise, 
 > even to write the topology by hand.  See the manual.

I just check the ffG53a6.rtp and I found that DPPC have an alkane chain. In my case          n-heptane. I followed the same idea you gave me for generating the toluene topology from PHE.  I made an entry to the .rtp using DPPC.

  pdb2gmx -f Heptane.pdb -o Heptane.gro -p Heptane.top -missing

  I got the topology from this force filed. Is this RIGHT!

Second, I am using the GROMOS96 ... ffG43a1 for my entire MD simulation since I am using as well PRODRG topology file for my polymors. In order to be consistent in all my simulation. I am using the ffG43a1 force field for heptane. Now I took the charge and charge group ONLY from ffG53a6.rtp of the DPPC and encorporate into the PRODRG.. to get a better topology. Is this the right thing to do. Please comment 

Third, how to avoid using a large tau_p. Like tau_p=3 for example. I tried tau_p=1 but it does not look working. I got this error.

Fatal error:
Too many LINCS warnings (1663)
If you know what you are doing you can adjust the lincs warning threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

But as soon as i changed its value. The MD is still running. Please comment.

Fouth, about the solvent box. when I fill my box that contain 8 polymers. What density do i need to keep for my mixture. By changing the solvent box I can change the entire density of the BOX of the actual simulation. what is the correct way of handling density.

Regards,

R

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> teklebrh at ualberta.ca wrote:
>> Dear Justin.
>>
>> I turned off the gen-vel to no. Yes you are right. But I got the same error.
>>
>> I increase tau-p ( from 1 to 3) and it looks working fine so far.
>>
>> One of the warnings is that the pressure is less 1%.
>>
>
> It could be that your previous equilibration was a bit insufficient 
> to relax whatever the system is so there are still some colliding 
> particles that cause the temperature to spike.  Increasing tau_p 
> makes the coupling a bit weaker, allowing for some greater 
> fluctuation, but you still may run into problems.
>
>> Thank you for your help Justine.
>>
>> ================================
>>
>> Remark from the previous request
>>
>> The pdb2gmx is also working .... the reinstalled the .rtp file and it is ok!
>>
>> I got the Toluene topology from the PHE.
>>
>> ===================================
>>
>> I want the same for the n-heptane toplogy using the pdb2gmx.... is 
>> there any method I could get that from the gromos96 force filed. 
>> Just to avoid using PRODRG!
>>
>
> To use pdb2gmx, you need an .rtp entry.  For something like 
> united-atom n-heptane, this should be a relatively easy exercise, 
> even to write the topology by hand.  See the manual.
>
> -Justin
>
> -- 
> ========================================
>
> Justin A. Lemkul
> 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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