# Query regarding solvation

**URL:** <https://gromacs.bioexcel.eu/t/query-regarding-solvation/608>\
**Category:** User discussions\
**Created:** [July 31, 2020, 3:00pm UTC](https://gromacs.bioexcel.eu/t/query-regarding-solvation/608 "2020-07-31T15:00:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![snehasis.chatterjee](https://avatars.discourse-cdn.com/v4/letter/s/90db22/32.png) [@snehasis.chatterjee](https://gromacs.bioexcel.eu/u/snehasis.chatterjee)\
**Post date:** [July 31, 2020, 3:00pm UTC](https://gromacs.bioexcel.eu/t/query-regarding-solvation/608/1 "2020-07-31T15:00:30Z")

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Dear Gromacs users,

I am trying to perform a simulation for a full capsid using GROMACS 2019. After generating topology of the full capsid using pdb2gmx, I solvated capsid using gmx solvate and add ions using gmx genion. Before production run, I did constant NVT (10 ns) and NPT (10 ns), where heavy atoms of the capsid are restrained. From constant NVT and NPT trjectories, I checked water density inside capsid. It is ~ 0.93 gm/ml. After that, I removed restrain in a stepwise manner.

During production run, I saw sudden decrease of radius of gyration of capsid within first 2-3 step of production run. Radius of gyration decrease from 13.85 nm to 13.75 nm. Water density inside capsid is ~ 1.0 gm/ml. My understanding is that capsid collapse happens due to less number of water molecule inside capsid during equilibration. But, I followed steps mentioned in the lysozyme tutorial. I am confused at this point.

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,  
Snehasis Chatterjee