[gmx-users] Error message

Hi, I am simulating a water droplet in gas phase using Gromacs. Basically, this is a water droplet kept at the centre of a large box of dimension 100 nm. The problem is that the run ended with an error message as shown below: “8 particles communicated to PME rank 14 are more than 2/3 times

Re: [gmx-users] error message: Invalid transform ...

x-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] error message: Invalid transform ... > > Message-ID: > >

Re: [gmx-users] error message: Invalid transform ...

> Message: 2 > Date: Fri, 28 Jul 2017 07:10:57 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] error message: Invalid transform ... > Message-ID: >

Re: [gmx-users] error message: Invalid transform ...

Hi, That's a new one for me ;-) So new that I assume you were changing the code? Mark On Fri, 28 Jul 2017 00:51 Clinton King wrote: > Has anybody ever seen the following error message before? > > > Program: gmx mdrun, version 2016.1 > Source file:

[gmx-users] error message: Invalid transform ...

Has anybody ever seen the following error message before? Program: gmx mdrun, version 2016.1 Source file: src/gromacs/fft/parallel_3dfft.cpp (line 173) *Fatal error:* *Invalid transform. Plan and execution don't match regarding reel/complex* -- Clinton King Graduate Student Chemistry

Re: [gmx-users] Error message

> Atomtype NRP not found > > Akash > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 18 May 2017 18:03 > To: gmx-us...@groma

Re: [gmx-users] Error message

-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 18 May 2017 18:03 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error message Hi, A molecule itp does not stand in isolation. >From that link "If the d

Re: [gmx-users] Error message

0 > O2CM 8 15.9994 0.0A 0.3029050.502080 > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin > Lemkul > Sent: 18 May 2017 17:00 > To: gm

Re: [gmx-users] Error message

...@gromacs.org Subject: Re: [gmx-users] Error message On 5/18/17 11:57 AM, Pandya, Akash wrote: > Hi all, > > I've been trying to figure out the error message below but I'm not getting > anywhere. I have attached my relevant itp file. Please could someone tell me > what is wrong w

Re: [gmx-users] Error message

On 5/18/17 11:57 AM, Pandya, Akash wrote: Hi all, I've been trying to figure out the error message below but I'm not getting anywhere. I have attached my relevant itp file. Please could someone tell me what is wrong with my itp file? Googling the error usually turns something up...

[gmx-users] Error message

Hi all, I've been trying to figure out the error message below but I'm not getting anywhere. I have attached my relevant itp file. Please could someone tell me what is wrong with my itp file? Fatal error: Syntax error - File GLY.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for

Re: [gmx-users] Error message while running energy minimization

I am trying to use ATB to generate topologies by no entries for mass values? I had chopped out the rest as it was exceeding the size. Would you suggest any other ligand topologies program? *Deep S Bhattacharya* Graduate Research Assistant, Department of Pharmaceutical sciences, University of

Re: [gmx-users] Error message while running energy minimization

On 7/13/16 2:05 PM, Deep Bhattacharya wrote: Can I use ATB topology for GROMOS53a6 forcefield? That's certainly a better source. Please refer to existing (and ongoing) threads regarding ATB, ligand topologies, etc. -Justin Deep On Wed, Jul 13, 2016 at 12:52 PM, Justin Lemkul

Re: [gmx-users] Error message while running energy minimization

Can I use ATB topology for GROMOS53a6 forcefield? Deep On Wed, Jul 13, 2016 at 12:52 PM, Justin Lemkul wrote: > > > On 7/13/16 1:48 PM, Deep Bhattacharya wrote: > >> Thanks. So I was looking at my ligand topology for the largest charged >> group, it is the SDmso type of atom.

Re: [gmx-users] Error message while running energy minimization

On 7/13/16 1:48 PM, Deep Bhattacharya wrote: Thanks. So I was looking at my ligand topology for the largest charged group, it is the SDmso type of atom. This was generated using PRODRG How can I fix this if this is the issue? [ atoms ] ; nr type resnr resid atom cgnr charge

Re: [gmx-users] Error message while running energy minimization

On 7/13/16 1:19 PM, Deep Bhattacharya wrote: I modified the em.mdp file ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol =

Re: [gmx-users] Error message while running energy minimization

I modified the em.mdp file ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum

Re: [gmx-users] Error message while running energy minimization

On 7/13/16 1:05 PM, Deep Bhattacharya wrote: I am using GROMACS v.4.6. Does using Verlet cut-off scheme lead to problems like blowing up of the system? No, you can't blame crashes on the Verlet algorithm. It should be more accurate than anything else. Systems typically crash because of

Re: [gmx-users] Error message while running energy minimization

I am using GROMACS v.4.6. Does using Verlet cut-off scheme lead to problems like blowing up of the system? When you say the largest charge in the topology you mean the combined protein-ligand pdb? I have attached the .top and combined pdb file. Please help Deep On Wed, Jul 13, 2016 at 11:56 AM,

Re: [gmx-users] Error message while running energy minimization

On 7/13/16 12:25 PM, Deep Bhattacharya wrote: Hello, This is the error message that I am getting trying to run energy minimization It's not an error, it's a note. That means, "for your information, here is something you may want to check." It does not necessarily mean anything is wrong

Re: [gmx-users] Error message in Energy minimization

It did run but it gave a note NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off

Re: [gmx-users] Error message in Energy minimization

Yes, that is possible. It should run. Evan L. On Jul 13, 2016 9:47 AM, "Deep Bhattacharya" < deep.bhattacharya1...@gmail.com> wrote: > > That would be rcoulumb rvdw and rlist at 1.4. > Is that possible? > > Deep > > Sent from my iPhone > > > On Jul 13, 2016, at 10:45 AM, Evan Lowry

Re: [gmx-users] Error message in Energy minimization

That would be rcoulumb rvdw and rlist at 1.4. Is that possible? Deep Sent from my iPhone > On Jul 13, 2016, at 10:45 AM, Evan Lowry wrote: > > Set rcoulomb=rlist and retry the minimization. > > Evan L. > On Jul 13, 2016 9:38 AM, "Deep Bhattacharya"

Re: [gmx-users] Error message in Energy minimization

Set rcoulomb=rlist and retry the minimization. Evan L. On Jul 13, 2016 9:38 AM, "Deep Bhattacharya" wrote: > Hello, > > This is the error message that I am getting trying to run energy > minimization > > ERROR 1 [file em.mdp]: > With coulombtype = PME (without

[gmx-users] Error message in Energy minimization

Hello, This is the error message that I am getting trying to run energy minimization ERROR 1 [file em.mdp]: With coulombtype = PME (without modifier), rcoulomb must be equal to rlist, or rlistlong if nstcalclr=1. For optimal energy conservation,consider using a potential modifier.

Re: [gmx-users] Error message in GROMACS

On 2015-01-14 10:22, Deep Bhattacharya wrote: Respected Sir, I have read up a lot on GROMACS webpages and the problems answered by you are extremely helpful. I have been facing this problem in computing violations of distance restraints and I get this error message , I will be extremely glad

[gmx-users] error message in mdrun: Check for bad contacts and/or reduce the timestep if appropriate.

Hi friends, I am calculating free energy of a protein. I got this message when i run mdrun. My command was mdrun -deffnm npt -nt 1 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.22, max 0.000500 (between atoms 2240 and 2243) bonds that rotated more