Re: [gmx-users] simulation error
On 9/18/18 11:55 AM, Mario Andres Rodriguez Pineda wrote: when i try to run mdrun they start showing this: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom= 2881 Step=1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom= 2881 Step=2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom= 2881 Step=3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom= 2881 Step=4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom= 2881 Step=5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom= 2881 Step=6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom= 2881 Step=7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom= 2881 Step=8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom= 2881 Step=9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom= 2881 Step= 10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom= 2881 Step= 11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom= 2883 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom= 2903 Step= 13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom= 2883 Step= 14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom= 2883 Step= 15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom= 2881 step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) I don't understand what happend. Please can you help me? How i can reduce timestep? You're stuck at a huge force on atom 2881. Check on what that is, what's around it, etc. If necessary, you can reduce emstep (energy minimization step size, not dt which is the time step in MD) to a smaller value. I don't think that's going to be an effective fix here. EM is clearly stuck trying to resolve something bad in your structure and it can't do it. -Justin Em ter, 18 de set de 2018 às 08:36, Justin Lemkul escreveu: On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: These were the errors until the moment of executing the minimization: After adding ions grompp: NOTE 1 [file topol.top, line 37566]: System has non-zero total charge: -18.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. minimization mdrun step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) In attach send you the mdp archive for minimization run. The mailing list does not allow attachments. Use the -v flag of mdrun to track the energy and forces at every step until the crash to see what's going on and where the maximum force is acting. There's probably a bad contact somewhere that can't be relaxed and you need to investigate why that's happening. -Justin Thanks for your help Em seg, 17 de set de 2018 às 19:56, Justin Lemkul escreveu: On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) Water SETTLE problems are not unusual in energy minimization and are often resolved. If, however, such a message immediately precedes a failure, then you have a serious problem with either the coordinates or topology. mdrun prints out which atom is experiencing the maximum force, so start by looking there, as well as reviewing your notes about what warnings pdb2gmx or grompp may have issued (but surely you wouldn't have ignored any, right? :). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 http://www.gromacs.org/Support/Mailin
Re: [gmx-users] simulation error
when i try to run mdrun they start showing this: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom= 2881 Step=1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom= 2881 Step=2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom= 2881 Step=3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom= 2881 Step=4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom= 2881 Step=5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom= 2881 Step=6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom= 2881 Step=7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom= 2881 Step=8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom= 2881 Step=9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom= 2881 Step= 10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom= 2881 Step= 11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom= 2883 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom= 2903 Step= 13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom= 2883 Step= 14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom= 2883 Step= 15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom= 2881 step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) I don't understand what happend. Please can you help me? How i can reduce timestep? Em ter, 18 de set de 2018 às 08:36, Justin Lemkul escreveu: > > > On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: > > These were the errors until the moment of executing the minimization: > > > > After adding ions grompp: > > NOTE 1 [file topol.top, line 37566]: > >System has non-zero total charge: -18.99 > >Total charge should normally be an integer. See > >http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > >for discussion on how close it should be to an integer. > > > > minimization mdrun > > step 16: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > tMPI error: Receive buffer size too small for transmission (in valid > comm) > > Abort (core dumped) > > > > In attach send you the mdp archive for minimization run. > > The mailing list does not allow attachments. > > Use the -v flag of mdrun to track the energy and forces at every step > until the crash to see what's going on and where the maximum force is > acting. There's probably a bad contact somewhere that can't be relaxed > and you need to investigate why that's happening. > > -Justin > > > Thanks for your help > > > > Em seg, 17 de set de 2018 às 19:56, Justin Lemkul > > escreveu: > > > >> > >> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > >>> Hi everyone. > >>> I'm trying simulate a protein in water followin lysozyme tutorial using > >>> gromacs 2016.3. When triying minimize the system after make the box and > >>> insert a salt concentration the minimization has been stoped sendingme > >> the > >>> following error: > >>> > >>> step 16: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> Wrote pdb files with previous and current coordinates > >>> tMPI error: Receive buffer size too small for transmission (in valid > >> comm) > >>> Abort (core dumped) > >> Water SETTLE problems are not unusual in energy minimization and are > >> often resolved. If, however, such a message immediately precedes a > >> failure, then you have a serious problem with either the coordinates or > >> topology. mdrun prints out which atom is experiencing the maximum force, > >> so start by looking there, as well as reviewing your notes about what > >> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have > >> ignored any, right? :). > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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 http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/grom
Re: [gmx-users] simulation error
On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: These were the errors until the moment of executing the minimization: After adding ions grompp: NOTE 1 [file topol.top, line 37566]: System has non-zero total charge: -18.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. minimization mdrun step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) In attach send you the mdp archive for minimization run. The mailing list does not allow attachments. Use the -v flag of mdrun to track the energy and forces at every step until the crash to see what's going on and where the maximum force is acting. There's probably a bad contact somewhere that can't be relaxed and you need to investigate why that's happening. -Justin Thanks for your help Em seg, 17 de set de 2018 às 19:56, Justin Lemkul escreveu: On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) Water SETTLE problems are not unusual in energy minimization and are often resolved. If, however, such a message immediately precedes a failure, then you have a serious problem with either the coordinates or topology. mdrun prints out which atom is experiencing the maximum force, so start by looking there, as well as reviewing your notes about what warnings pdb2gmx or grompp may have issued (but surely you wouldn't have ignored any, right? :). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation error
These were the errors until the moment of executing the minimization: After adding ions grompp: NOTE 1 [file topol.top, line 37566]: System has non-zero total charge: -18.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. minimization mdrun step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) In attach send you the mdp archive for minimization run. Thanks for your help Em seg, 17 de set de 2018 às 19:56, Justin Lemkul escreveu: > > > On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everyone. > > I'm trying simulate a protein in water followin lysozyme tutorial using > > gromacs 2016.3. When triying minimize the system after make the box and > > insert a salt concentration the minimization has been stoped sendingme > the > > following error: > > > > step 16: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > tMPI error: Receive buffer size too small for transmission (in valid > comm) > > Abort (core dumped) > > Water SETTLE problems are not unusual in energy minimization and are > often resolved. If, however, such a message immediately precedes a > failure, then you have a serious problem with either the coordinates or > topology. mdrun prints out which atom is experiencing the maximum force, > so start by looking there, as well as reviewing your notes about what > warnings pdb2gmx or grompp may have issued (but surely you wouldn't have > ignored any, right? :). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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 http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation error
On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) Water SETTLE problems are not unusual in energy minimization and are often resolved. If, however, such a message immediately precedes a failure, then you have a serious problem with either the coordinates or topology. mdrun prints out which atom is experiencing the maximum force, so start by looking there, as well as reviewing your notes about what warnings pdb2gmx or grompp may have issued (but surely you wouldn't have ignored any, right? :). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation error
Hi Reduce your timestep and see as it is suggested. Best On Mon, Sep 17, 2018 at 5:48 PM Mario Andres Rodriguez Pineda < mand...@iq.usp.br> wrote: > Hi everyone. > I'm trying simulate a protein in water followin lysozyme tutorial using > gromacs 2016.3. When triying minimize the system after make the box and > insert a salt concentration the minimization has been stoped sendingme the > following error: > > step 16: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > tMPI error: Receive buffer size too small for transmission (in valid comm) > Abort (core dumped) > > How i can fix it? > Thanks for your help. > > -- > *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* > *Estudiante Doctorado en Biotecnología* > *UNAL- MEDELLÍN * > -- > 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 http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simulation error
Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) How i can fix it? Thanks for your help. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
