Dear Justin,
Thank you for your suggestions! So what I have done is right. For implicit
solvent, I just need turn on the options in .mdp file and no .itp file is
needed to be included in the topology file. (I have tried but get errors).
Thanks!
Regards,
Zhuo
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On 10/7/19 11:12 AM, zhangzhu...@hotmail.com wrote:
Dear Paul,
Thanks for your advice. Since my system is acidic, I thought implicit solvent
would get better approximation as I read from the GROMACS website. So there was
no idea about my problem?
Implicit solvent is used without PBC and
Dear Paul,
Thanks for your advice. Since my system is acidic, I thought implicit solvent
would get better approximation as I read from the GROMACS website. So there was
no idea about my problem?
Thanks!
Zhuo
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Hi, I am doing the aggregations of small peptides in implicit solvents.
However, it seems that there is no detailed tutorial on such subject and I just
turned on the 'implicit solvent' option in the .mdp file. However, I found that
the box was compressed during mdrun. It comes to me that the
Hello,
the implicit solvent functionality has been deprecated a while ago in
GROMACS and has been removed in the recent versions.
Can the simulations also be run in explicit solvents (that are a better
physical representation anyway)?
Cheers
Paul
On 07/10/2019 16:50, 张 卓 wrote:
Hi, I am
Hi, I am doing the aggregations of small peptides in implicit solvents.
However, it seems that there is no detailed tutorial on such subject and I just
turned on the 'implicit solvent' option in the .mdp file. However, I found that
the box was compressed during mdrun. It comes to me that the
