Dear all,
I want to simulate a polyelectrolyte with its counterions( five chain and 200 ions). I did distance restrain between ions and (N+) in the polymer chain. In NPT level my system is not stabilized and I face with Errors like:
Step 34, time 0.034 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000318, max 0.005474 (between atoms 1553 and 1552)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1553 1552 70.0 0.1054 0.1005 0.1000
I think it is because of distance restrain.is it true? because in the case without restrain I didn't encountered with such error.
my question is that is distance restrain necessary in NPT level for simulation? I want to calculate density in bulk mode(without any solvent) and in NVT level ions were close enough to (N+).
any response would be greatly appreciated.
Wow, LINCS error. It often rises just before your system blows up. There must be some significant unfavorable interactions in your system. You need to check it visually. Often these is no difference between NVT and NPT simulations. They are the same thermodynamic ensemble but the algorithms used to maintain the pressure might sometimes cause some problems. In most cases, the current instability problem is just caused by your system and setup.
Wow, LINCS error. It often rises just before your system blows up. There must be some significant unfavorable interactions in your system. You need to check it visually. Often these is no difference between NVT and NPT simulations. They are the same thermodynamic ensemble but the algorithms used to maintain the pressure might sometimes cause some problems. In most cases, the current instability problem is just caused by your system and setup.
Wow, LINCS error. It often rises just before your system blows up. There must be some significant unfavorable interactions in your system. You need to check it visually. Often these is no difference between NVT and NPT simulations. They are the same thermodynamic ensemble but the algorithms used to maintain the pressure might sometimes cause some problems. In most cases, the current instability problem is just caused by your system and setup.
Zhaoxi Sun
Dear Sun
Thank you very much for your response. then a well relaxed structure avoid such error. and I think I have to modify some parts of my force field.
Thank you again for your kind response
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