I have a modeled structure of RNA with 25 nts. I have renamed the atoms as per the rtp file of the amber99sb-ildn force field. All the steps upto energy minimisation ran without any error. The equillibration step with NVT of 200ps is running extremely slow. I have already run a protein (90 aa long) simulation with exact same parameters which completed NVT in 10 mins. I have no clue where things are going wrong.
p.s. I found it odd that the topol.top file generating after the command: gmx pdb2gmx -f rna.pdb -o rna.gro (with -ff amber99sb-ildn and -water tip4p) is showing system name as 'protein'!
The last few lines of the topol.top file is:
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
RNA_chain_A 1
Due to this rna_solv_ions.gro shows system name as 'Protein in water'
I don't know if it is relevant to the problem but I found this odd. As if, pdb2gmx cannot recognize my pdb file as a proper RNA molecule!
Kindly help me to understand the issue and resolve it.
Thanks in advance.
The system name written by pdb2gmx is irrelevant. It's just a placeholder.
Performance cannot necessarily be compared between systems. How fast the simulation proceeds depends on number of atoms (which is a function of the solute size, not necessarily length), chosen water model (you have a 4-point model here, which will be somewhat slow) and how you're utilizing available hardware. The .log file prints tons of performance information so you can tell why you got the performance you did.
Justin Lemkul Thank you so much for your response. It was the hardware which made the difference. Its running fine now. Though, thanks once again for your insight.
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