Re: [gmx-users] simulation crashed because of LINCS error
sonali dhindwal wrote:
Thanks Mark for the reply,
I think I have mistakenly written 30 instead of 300 for ref_t in temp
coupling,
So if that could be the problem ?
because I have equilbrated the protein before simulation but time is
for 20 ps. Is that very short time period?
Acually I want to stress here that i have energy minimized the protein
by restraining the positions as i mentioned before to not to have large
changes in the protein structure, and then again equilibration and
simulation was carried our by constraining all the bonds. So if that is
ok to do ?
I remember your rationale for restraints during EM was to avoid distortions in
the structure, and the consensus that you got was that there was nothing wrong
with your results. Restraints actually serve to prevent atoms from moving, thus
defeating the purpose of EM. Repeat the EM without restraints. Your structure
is likely not sufficiently energy-minimized to continue.
-Justin
Regards
--
Sonali Dhindwal
--- On *Mon, 24/5/10, Mark Abraham //* wrote:
From: Mark Abraham
Subject: Re: [gmx-users] simulation crashed because of LINCS error
To: "Discussion list for GROMACS users"
Date: Monday, 24 May, 2010, 1:00 PM
- Original Message -
From: sonali dhindwal >
Date: Monday, May 24, 2010 14:32
Subject: [gmx-users] simulation crashed because of LINCS error
To: Discussion list for GROMACS users >
---
| > Hello All,
>
> With regard to my previous post
> http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html
> I have done postion restrained energy minimisation using
POSRES.itp file obtained from pdb2gmx. so that there should not be
any large change in the strucutre of the protein.
Note that there are further general recommendations about system
preparation here
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation,
i.e. consider not going immediately to your target ensemble.
Also, your temperature-coupling is broken in your second .mdp file.
Mark
> And after that I did equilbration using following mdp file
>
> title = protein
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator =
md
> dt = 0.002 ; ps !
> nsteps = 1 ; total 20.0 ps.
> nstcomm = 1
> nstxout = 250 ; collect data every 0.5 ps
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist =
5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb= 0.9
> rvdw= 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft= yes
> ; Berendsen temperature
coupling is on in two groups
> Tcoupl = V-rescale
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300
K.
> gen_vel = yes
> gen_temp= 300.0
> gen_seed= 173529
>
> After this, I put the molecule for simulation using the following
.mdp file
>
> title = protein
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 50 ; total 1000 ps, 1
ns.
> nstcomm = 1
> nstxout = 500 ; collect data every 1 ps
> nstvout = 0
> nstfout = 0
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb= 0.9
> rvdw=
1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft= yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl
Re: [gmx-users] simulation crashed because of LINCS error
Thanks Mark for the reply, I think I have mistakenly written 30 instead of 300 for ref_t in temp coupling, So if that could be the problem ? because I have equilbrated the protein before simulation but time is for 20 ps. Is that very short time period? Acually I want to stress here that i have energy minimized the protein by restraining the positions as i mentioned before to not to have large changes in the protein structure, and then again equilibration and simulation was carried our by constraining all the bonds. So if that is ok to do ? Regards -- Sonali Dhindwal --- On Mon, 24/5/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] simulation crashed because of LINCS error To: "Discussion list for GROMACS users" Date: Monday, 24 May, 2010, 1:00 PM - Original Message - From: sonali dhindwal Date: Monday, May 24, 2010 14:32 Subject: [gmx-users] simulation crashed because of LINCS error To: Discussion list for GROMACS users --- | > Hello All, > > With regard to my previous post > http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html > I have done postion restrained energy minimisation using POSRES.itp file > obtained from pdb2gmx. so that there should not be any large change in the > strucutre of the protein. Note that there are further general recommendations about system preparation here http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation, i.e. consider not going immediately to your target ensemble. Also, your temperature-coupling is broken in your second .mdp file. Mark > And after that I did equilbration using following mdp file > > title = protein > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 1 ; total 20.0 ps. > nstcomm = 1 > nstxout = 250 ; collect data every 0.5 ps > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > After this, I put the molecule for simulation using the following .mdp file > > title = protein > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 50 ; total 1000 ps, 1 ns. > nstcomm = 1 > nstxout = 500 ; collect data every 1 ps > nstvout = 0 > nstfout = 0 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 30 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > but simulation has crashed showing the error too many Too many LINCS warnings > (1000) > I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. > So can you please help me in correcting it. > Thanks and regards. > > -- > Sonali Dhindwal | --- > > -- > gmx-users mailing
Re: [gmx-users] simulation crashed because of LINCS error
- Original Message - From: sonali dhindwal Date: Monday, May 24, 2010 14:32 Subject: [gmx-users] simulation crashed because of LINCS error To: Discussion list for GROMACS users --- | > Hello All, > > With regard to my previous post > http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html > I have done postion restrained energy minimisation using POSRES.itp file > obtained from pdb2gmx. so that there should not be any large change in the > strucutre of the protein. Note that there are further general recommendations about system preparation here http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation, i.e. consider not going immediately to your target ensemble. Also, your temperature-coupling is broken in your second .mdp file. Mark > And after that I did equilbration using following mdp file > > title = protein > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 1 ; total 20.0 ps. > nstcomm = 1 > nstxout = 250 ; collect data every 0.5 ps > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > After this, I put the molecule for simulation using the following .mdp file > > title = protein > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 50 ; total 1000 ps, 1 ns. > nstcomm = 1 > nstxout = 500 ; collect data every 1 ps > nstvout = 0 > nstfout = 0 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 30 > ; Pressure coupling is on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > but simulation has crashed showing the error too many Too many LINCS warnings > (1000) > I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. > So can you please help me in correcting it. > Thanks and regards. > > -- > Sonali Dhindwal | --- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation crashed because of LINCS error
Hello All, With regard to my previous post http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html I have done postion restrained energy minimisation using POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein. And after that I did equilbration using following mdp file title = protein cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 After this, I put the molecule for simulation using the following .mdp file title = protein cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50 ; total 1000 ps, 1 ns. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 30 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 but simulation has crashed showing the error too many Too many LINCS warnings (1000) I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. So can you please help me in correcting it. Thanks and regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
