<p class="imp-signature"><!--begin_signature--><!--end_signature--></p>Dear Justin,<br /> <br /><span style="color: #1012ff;">> To use pdb2gmx, you need an .rtp entry. For something like </span><br style="color: #1012ff;" /><span style="color: #1012ff;">
> united-atom n-heptane, this should be a relatively easy exercise, </span><br style="color: #1012ff;" /><span style="color: #1012ff;">
> even to write the topology by hand. See the manual</span>.<br /> <br />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.<br /><br /> pdb2gmx -f Heptane.pdb -o Heptane.gro -p Heptane.top -missing<br /><br /> I got the topology from this force filed. Is this RIGHT!<br /><br />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 <br /><br />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.<br /><br />Fatal error:<br />Too many LINCS warnings (1663)<br />If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br />or set the environment variable GMX_MAXCONSTRWARN to -1,<br />but normally it is better to fix the problem<br /><br />But as soon as i changed its value. The MD is still running. Please comment.<br /><br />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.<br /><br />Regards,<br /><br />R<br /><br /><br />
Quoting "Justin A. Lemkul" <jalemkul@vt.edu>:<br /> <br />
><br />
><br />
> teklebrh@ualberta.ca wrote:<br />
>> Dear Justin.<br />
>><br />
>> I turned off the gen-vel to no. Yes you are right. But I got the same error.<br />
>><br />
>> I increase tau-p ( from 1 to 3) and it looks working fine so far.<br />
>><br />
>> One of the warnings is that the pressure is less 1%.<br />
>><br />
><br />
> It could be that your previous equilibration was a bit insufficient <br />
> to relax whatever the system is so there are still some colliding <br />
> particles that cause the temperature to spike. Increasing tau_p <br />
> makes the coupling a bit weaker, allowing for some greater <br />
> fluctuation, but you still may run into problems.<br />
><br />
>> Thank you for your help Justine.<br />
>><br />
>> ================================<br />
>><br />
>> Remark from the previous request<br />
>><br />
>> The pdb2gmx is also working .... the reinstalled the .rtp file and it is ok!<br />
>><br />
>> I got the Toluene topology from the PHE.<br />
>><br />
>> ===================================<br />
>><br />
>> I want the same for the n-heptane toplogy using the pdb2gmx.... is <br />
>> there any method I could get that from the gromos96 force filed. <br />
>> Just to avoid using PRODRG!<br />
>><br />
><br />
> To use pdb2gmx, you need an .rtp entry. For something like <br />
> united-atom n-heptane, this should be a relatively easy exercise, <br />
> even to write the topology by hand. See the manual.<br />
><br />
> -Justin<br />
><br />
> -- <br />
> ========================================<br />
><br />
> Justin A. Lemkul<br />
> MILES-IGERT Trainee<br />
> Department of Biochemistry<br />
> Virginia Tech<br />
> Blacksburg, VA<br />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> <a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br />
><br />
> ========================================<br />
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