Re: [gmx-users] Energy Minimization Error

Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin

Re: [gmx-users] Energy Minimization Error

On 10/19/17 8:21 PM, Amali Guruge wrote: Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? That happens often during

Re: [gmx-users] Energy Minimization Error

Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul

Re: [gmx-users] Energy Minimization Error

On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm,

Re: [gmx-users] energy minimization error

Hi, Thanks a lot for your time and patience. This time, I chose a very simple structure and then inspected the generated topology. The interesting point was that, there were some missing interactions. When I inspected them. I found that I had defined those interactions in ffbonded.itp file, but

Re: [gmx-users] energy minimization error

Hi, pdb2gmx and grompp are pretty talkative about things like missing parameters and bonds - go back and read what they had to say, and particularly what pdb2gmx thought about your specbonds. Mark On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani wrote: > Hi, > >

Re: [gmx-users] energy minimization error

Hi, Did you inspect your topology like I suggested? You need to know that there are bonds exactly where you intend them, before doing any calculations with them. Mark On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani wrote: > Hi, > > I am trying to simulate a

Re: [gmx-users] Energy minimization error

Hi, As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and

Re: [gmx-users] Energy minimization error

Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps

Re: [gmx-users] Energy minimization error

Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply

Re: [gmx-users] Energy minimization error

Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this

Re: [gmx-users] energy minimization error

Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com wrote: Hi Justin, I have asked this before, but this time I started up from scratch and

Re: [gmx-users] energy minimization error

On 6/27/15 2:29 AM, James Lord wrote: Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * The DD errors have nothing to do with physical stability; you just can't necessarily parallelize any arbitrary system over any arbitrary

Re: [gmx-users] energy minimization error

On 6/26/15 7:19 PM, James Lord wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the

Re: [gmx-users] energy minimization error

Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined?

Re: [gmx-users] energy minimization error

On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based

Re: [gmx-users] energy minimization error

On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8

Re: [gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

On 4/28/15 8:14 AM, Abhijit Jassem wrote: Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s