Getting error using "gmx clustsize" tool with -mol yes flag on

I need to measure the aggregation of a type of molecule. The aggregation will happen if the COM of molecules becomes less than 0.85 nm. I think I should use g_clustsize but it normally calculates clusters based on the atoms. there is "-mol" as an option to change the calculation basis from atom to molecule but I am not sure if it considers the center of mass of molecule! Also, there is no option to change the cutoff.

There is another keyword, "cluster", that calculate RMSD between structures to realize if they form a cluster or not. This keyword has the cutoff option but the same as the previous one, I can not make sure if the RMSD is calculated between COMs.

I wonder if anyone can help me with this problem

Hi all,

Currently I am working with CG- Mie potentials and I have obtained good results, but option clustsize doesn't work well for me after simulation. I think that the problem could be in the .mdp production file which I attach here, do you see where could be my mistake?

thanks a lot

I used "draw delete all" command to delete the pbc box in VMD, but it's just removed from the current frame. How can I remove it from all frames?

Dear researcher,

                           I am a learner of Gromacs. I want to simulate my protein in different pH. in .mdp file i did not saw any option to define the pH.

please suggest me how can i set the pH

How could I extract the total number of clusters over time?  

A swift search in gmx-mail.list suggested using the output of -clid plus simple scripting. Further details will be valuable.

I am trying to run an md simulation for 1ns for energy minimization of a pdb structure but everytime after 129 steps it fails with the error Too many Lincs Warning. What is the problem in simulation I dont know. Someone please help with this

How could I determine the cluster size distribution of some molecules from MD simulation? Say that I have a simulation made of a ternary mixture A+B+C. Now say that A molecules tend to cluster together. I want to determine how many clusters and with how many A molecules are found in the trajectory by defining two A molecules to be in a cluster by one (or more) geometric conditions.

Is there any specific tool to do that (other than Gromacs g_cluster and/or g_clustsize)?

Thanks

I am working with gromacs and I have got a warning as shown below. Can you please suggest what to do to run my file completely. Please reply as soon as possible. I am awaiting your suggestions.

Step 8399 Warning: Pressure scaling more than 1%.

DD step 8399 vol min/aver 0.653 load imb.: force 1.2% pme mesh/force 0.756

Step Time Lambda

8400 16.80000 0.00000

Step 8400 Warning: Pressure scaling more than 1%.

Energies (kJ/mol)

Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14

2.54157e+05 1.41582e+04 1.06152e+05 1.08902e+05 4.41780e+05

LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.

4.77747e+05 -2.47518e+05 -2.41742e+07 -6.58090e+06 8.86258e+06

Potential Kinetic En. Total Energy Temperature Pres. DC (bar)

-2.07371e+07 9.08915e+05 -1.98282e+07 5.84109e+01 -4.79084e+02

Pressure (bar) Constr. rmsd

1.68607e+05 2.47297e-04

Does this mean that I did not run the energy minimization long enough and there are some high forces? Is there something else that I am doing wrong?

In my mdp file, the pressure coupling looks like:

; 7.3.15 Pressure Coupling

pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable

pcoupltype = isotropic ; pressure coupling in x-y-z directions

tau_p = 2.0 ; [ps] time constant for coupling

compressibility = 4.5e-5 ; [bar^-1] compressibility

ref_p = 1.0 ; [bar] reference pressure for coupling

Hi

I have a martini system of 1642 atoms. Most of them are overlapping. I tried running energy minimization with all sorts of parameter manipulation but system doesn't resolve and crashes. I am wondering if GROMACS provide soft potential function like LAMMPS to relax system before running real MD simulation. or there is any other way of removing overlaps?

Kindly help.

energy minimization Script I am using:

integrator = steep

dt = 0.010

nsteps = 100000

cutoff-scheme = Verlet

nstlist = 10

ns_type = grid

pbc = xyz

rlist = 1.4

coulombtype = reaction-field

rcoulomb_switch = 0.0

rcoulomb = 1.1

epsilon_r = 15

vdw_type = cutoff

vdw-modifier = Potential-shift-verlet

rvdw = 1.1