Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

-- From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Sent At:2019 Aug. 1 (Thu.) 12:31 To:gromacs ; 孙业平 Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs? Hi, Yes you can use the (-maxwarn)

Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

Hi, Yes you can use the (-maxwarn) flag to overcome the error. But better to optimize the starting structure to reduce the excess charge of your system. On Thu, Aug 1, 2019 at 9:35 AM sunyeping wrote: > Dear all, > > I am trying to do MD simulation with protein-DNA complex with gromacs. >

Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#system-has-non-zero-total-charge You will need to go through your topologies and work out why there is a non-zero charge like that. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

[gmx-users] How to deal with "non-zero total charge" problem in gromacs?

Dear all, I am trying to do MD simulation with protein-DNA complex with gromacs. When using gmx grompp to generate the tpr file for energy minimization, I enconters a fatal error: Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. There are

[gmx-users] OPLS parameterization for a modified aminoacid

Hello gromacs users, Do I use this reference for the procedure to find OPLS parameters for a modified aminoacid? Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum

Re: [gmx-users] Regarding OH, HH vector distribution

Den 2019-07-31 kl. 15:00, skrev Omkar Singh: I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Try write your own script. Thanks On Wed, Jul 31, 2019,

Re: [gmx-users] GROMOS 54a7 mapping warning

Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa: Hallo everyone, I want to simulate a peptide with the Gromos 54a7 force field. Your structure is missing atoms, please fix and rerun without -ignh. So, my first command is: gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh

Re: [gmx-users] Normal mode segmentation fault - memory problem ?

Hopefully I'm answering the right way. It also didn't work when using "-last 82737" and the segfault happened right after "will try to allocate memory and convert to full matrix representation". I don't get what I'm doing wrong here. Best, Marlon Sidore 06.69.24.81.94 PhD - Post-doctoral

[gmx-users] GROMOS 54a7 mapping warning

Hallo everyone, I want to simulate a peptide with the Gromos 54a7 force field. So, my first command is: gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the titratable amino acids and for the

Re: [gmx-users] Regarding OH, HH vector distribution

I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Thanks On Wed, Jul 31, 2019, 12:00 David van der Spoel wrote: > Den 2019-07-31 kl. 06:12, skrev Omkar

[gmx-users] gromacs pullcode

Hi,There are two  groups in my system.When I use the pull code to pull one group along the axis X, setting pull_coord1_geometry =direction-periodic,I am confused with the "distance at start" and the "reference at t=0".Could anyone can tell me how to understand these?And

Re: [gmx-users] Regarding OH, HH vector distribution

Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you How about gmx gangle