Re: [gmx-users] Lincs warning and Bond length not finite

Many thanks Alex for your reply :) You have pressure scaling and LINCS convergence issues, suggesting that > the starting configuration is far from equilibrium, as well as > potentially other issues. > > How to check if my starting configuration is far from equilibrium ? I checked the Temperature

Re: [gmx-users] Lincs warning and Bond length not finite

You have pressure scaling and LINCS convergence issues, suggesting that the starting configuration is far from equilibrium, as well as potentially other issues. Gromos FF is not appropriate for graphene, and neither is turning C-C bonds into LINCS constraints, as set by your 'all-bonds' --

[gmx-users] Lincs warning and Bond length not finite

Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got

Re: [gmx-users] Lincs warning in free energy calculation (FAISAL NABI)

Dear Gromacs users I am using amber99sb-ildn.ff force field for protein and I used GAFF for ligand parameterization. I tried different options e.g using constraint =all bonds as well as h-bonds. Reducing the time step to 1 fs but still, I could not solve the problem and get lincs warning

[gmx-users] lincs warning

Sent from Yahoo Mail on Android - Forwarded Message - From: "Afsane Farhadi" To: "gromacs.org_gmx-users@maillist.sys.kth.se" Cc: Sent: Mon, Apr 27, 2020 at 3:52 PM Subject: lincs warning Hi users I have two types of molecules ,methane and carbondioxide. i optimized them by

Re: [gmx-users] lincs warning

Hi Afsane, This might be an issue with the pressure coupling, depending on the compressibility you give for your system and the algorithm that you use for pressure coupling you might see quite large fluctuations in pressure. One idea might be to use temperature coupling to quickly dissipate

Re: [gmx-users] lincs warning

: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Afsane Farhadi Sent: Sunday, April 26, 2020 01:16 To: Discussion List for GROMACS Users Subject: [gmx-users] lincs warning Hi gromacs users I generated a mixed

[gmx-users] lincs warning

Hi gromacs users I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas  is ok (potential energy is about -2e+03))but when I want to run a npt run

Re: [gmx-users] Lincs warning in free energy calculation

Check the forcefield you are using is appropriate for your system or there might be some problem with the ligand parameters. On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote: > Dear Gromacs users > I ran an MD simulation for 3ns and from the last coordinates started a free > energy

[gmx-users] Lincs warning in free energy calculation

Dear Gromacs users I ran an MD simulation for 3ns and from the last coordinates started a free energy calculation for 3ns. My system is well equilibrated but after 710725 steps I am getting Lincs warning every time as below:- WARNING: There are no atom pairs for dispersion correction starting

Re: [gmx-users] Lincs warning

Dear Mark Thank you for your reply I resolved my problem by refining the output ot the tool Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] LINCS warning

Hi, I can't tell whether that's a periodicity artefact in your visualization, or the topology is indeed junk. You will likely need to inspect the output of the tool that generated it. Rarely do these things "just work." Mark On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli wrote: > Dear Mark >

Re: [gmx-users] LINCS warning

Dear Mark Thank you for your reply I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this results: EM results: Steepest Descents converged to machine precision in 80 steps, but did not reach the requested Fmax < 1000. Potential Energy = -3.4145945e+03 Maximum force =

Re: [gmx-users] LINCS warning

Hi, That tends to suggest either your ligand conformation or ligand parameters are not appropriate. What happens with ligand in vacuo with EM and then NVE with a very small time step, e.g. 0.5 ps? Mark On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli wrote: > Dear gromacs users > > I am

[gmx-users] LINCS warning

Dear gromacs users I am trying to simulate a complex, including a protein and a peptidec ligand with 2 phosphotyrosine residues. The protein topology was generated using amber99sb.ff in gromacs and the ligand topology was generated using ff99sb in amber tools 16, then the .inpcrd and .prmtop

Re: [gmx-users] LINCS WARNING during EPM2 CO2 Simulation

Hi, Simplify things until you identify the problematic part. Eg do one CO2 molecule first. Mark On Thu, 19 Oct 2017 03:16 Pimo Oni wrote: > Dear community members, > > Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while > I met continual LINCS

[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

Dear community members, Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while I met continual LINCS WARNING. I've been struggling for more than week but make no progress in fixing it.. : ( Here attach my pdb, top, and mdp files below. I would much appreciate any tip &

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

On 8/2/17 9:12 AM, Ali Ahmed wrote: Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title'

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off!

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

On 8/1/17 6:07 PM, Ali Ahmed wrote: Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support.

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information.

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham wrote: > Hi, > > Did you get any warnings from grompp? > > Mark > > On Mon, Jul 31, 2017 at

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hi, Did you get any warnings from grompp? Mark On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > Hello GROMACS users, > > I'm doing MD for nitrogen, and for better electrostatic interactions I need > to use massless and charged virtual site. I did that but when I try to

[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hello GROMACS users, I'm doing MD for nitrogen, and for better electrostatic interactions I need to use massless and charged virtual site. I did that but when I try to do energy minimization gives me LINCS warning and crush. I don't know where is the error I tried a lot but could not find a

Re: [gmx-users] LINCS warning during constrained md

Dear Mark, I understand your point, but I've used the Martini-backmapping protocol written in the initram.sh wrapper found in Martini documentation (https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it seems to me quite weird that it was not working in the proper manner. an

Re: [gmx-users] LINCS warning during constrained md

Hi, I would avoid using the combination of position restraints and constrained bonds with an input structure that is not necessarily consistent with the constraints. That's a recipe for large forces. I wouldn't use position restraints in such a process unless I had some reason to believe that my

Re: [gmx-users] LINCS warning during constrained md

hi, I've seen with vmd the gro file generated after the transformation, and after the 2 steps of minimization, it seems that they have no problem, while if I see the step_n.pdb file generated before the crash, there are some atoms far away from the rest of the protein, while this is not

Re: [gmx-users] LINCS warning during constrained md

Hi, Those are all good things, but have you actually got out a molecular viewer and looked at the input and output of your resolution conversion? Mark On Wed, Jul 12, 2017 at 4:25 PM edesantis wrote: > Hi, > thanks for the prompt answer, > > > I've found the same

Re: [gmx-users] LINCS warning during constrained md

Hi, thanks for the prompt answer, I've found the same problem even if I try to convert the coarse grained pdb obtained from martinize.py, so in that case it should be not a problem to have the conversion, for this reason I though it is a methodological problem... I've seen the blowing-up

Re: [gmx-users] LINCS warning during constrained md

Hi, Sounds like you might be http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the conversion doesn't work for your configuration. You should start by doing a visual check of the configuration for sanity, then follow the advice in that link. Mark On Wed, Jul 12, 2017 at 3:04

[gmx-users] LINCS warning during constrained md

dear all, I am facing a problem with the conversion from Martini CG representation to All-atomistic one. I am using the initram.sh wrapper around the backward.py. There is a LINCS warning problem when the energy relaxation is performed using position restrained md (I've also tried to run

Re: [gmx-users] lincs warning

On 3/14/17 2:57 AM, fatemeh ramezani wrote: Dear gmx usersplease help me if you know how can I change lincs warning threshold in mdp file or in command? The .mdp option is lincs-warnangle but you should not be toying with this option just to make errors go away; LINCS warnings indicate a

[gmx-users] lincs warning

Dear gmx usersplease help me if you know how can I change lincs warning threshold in mdp file or in command? thank you Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] LINCS warning

On 8/25/16 5:56 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello users, I was trying to energy minimize my system of protein embedded in bilayer. But I am receiving the following error: Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max

[gmx-users] LINCS warning

Hello users, I was trying to energy minimize my system of protein embedded in bilayer. But I am receiving the following error: Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max 0.149038 (between atoms 21616 and 21619) bonds that rotated more

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Hi Antara, What commands did you use? At least make sure you add -rdd 1.6 to the command line of mdrun, because the default value is too small for coarse grain simulations. Cheers, Tsjerk On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar wrote: > Dear users, > > I am

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Hi, Several things will make it easier to help - particularly your GROMACS versions and how you ran mdrun. See also http://www.gromacs.org/Support Mark On Fri, May 13, 2016 at 7:42 PM Antara mazumdar wrote: > Dear gromacs users, > > I am trying to run a coarse grained

[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Dear gromacs users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model. I have already performed all the equilibration steps successfully on my desktop. However, when i try to execute its production run in parallel it complains of

[gmx-users] LINCS warning of QMMM simulation

Dear gromacs users i was trying to simulate simple QMMM of 2-chlorobutanol versus protonated water... my simulation was going well until LINCS warning appeared. "Step 34, time 0.017 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.19, max 0.231421 (between atoms 2

[gmx-users] LINCS WARNING

Hi to all dear gmx users during the Energy Minimization i got this warning in first few steps after step 20 "step 20: Water molecule starting at atom 34209 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate." but after 3021 steps it was converged to Fmax < 1000.

Re: [gmx-users] LINCS WARNING

On 10/6/15 3:26 AM, Vy Phan wrote: Dear all gromacs Users! I want to run a simulation with the system protein-ligand (I have several ligands). With EM, nvt, npt step I put position restraint for the ligands and all thing was fine. After that, I run production simulation without position

[gmx-users] LINCS WARNING

Dear all gromacs Users! I want to run a simulation with the system protein-ligand (I have several ligands). With EM, nvt, npt step I put position restraint for the ligands and all thing was fine. After that, I run production simulation without position restraint of ligands. I saw the ligand move

Re: [gmx-users] LINCS WARNING

Dear Justin, I am so thankful for you kindly reply. Now, I can solve this problem. Tuong Vy On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul wrote: > > > On 10/6/15 3:26 AM, Vy Phan wrote: > >> Dear all gromacs Users! >> I want to run a simulation with the system protein-ligand

[gmx-users] LINCS WARNING

Hello Everyone I am simulation a protein as per the lysozyme tutorial. MY simulation got dumped at final mdrun step. It is showing following warning : Command line: gmx mdrun -deffnm md_0_1 Reading file md_0_1.tpr, VERSION 5.0.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads

Re: [gmx-users] LINCS WARNING

On 7/14/15 3:07 AM, Sun Iba wrote: Hello Everyone I am simulation a protein as per the lysozyme tutorial. MY simulation got dumped at final mdrun step. It is showing following warning : Command line: gmx mdrun -deffnm md_0_1 Reading file md_0_1.tpr, VERSION 5.0.5 (single precision) Using

Re: [gmx-users] LINCS warning

On 4/28/14, 1:37 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote: Dear Gromacs user, After I give the command for nvt, I get the following error: starting mdrun 'Protein in water' 15 steps,300.0 ps. Step 0, time 0 (ps) LINCS WARNING If the run crashes at step zero, it

[gmx-users] LINCS warning

Dear Gromacs user, After I give the command for nvt, I get the following error: starting mdrun 'Protein in water' 15 steps,300.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.410417, max 7.601056 (between atoms 188 and 192) bonds that rotated