Hi Xavier sir, Thanks for your valuable reply. How can I refine the non-bonded set-up ? And where can I specify the time step to 0.0001 ? I am new to gromacs. Sorry to ask such questions.
Thanking you, Pawan On Thu, Mar 19, 2009 at 2:54 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Doubt regarding membrane protein in POPC bilayer (Pawan Kumar) > 2. how to get the the force plot after pulling dynamic > simulation using GMX-3.3 (huifang liu) > 3. Re: Doubt regarding membrane protein in POPC bilayer > (XAvier Periole) > 4. RE: compressibility tensor components, pressure coupling > anisotropic PR, triclinic systems (Berk Hess) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Mar 2009 10:44:44 +0530 > From: Pawan Kumar <pawan.chin...@gmail.com> > Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer > To: gmx-users@gromacs.org > Message-ID: > <143b0c640903182214n2a603f97q478bfac66f502...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear gmx-users, > > Greetings from Pawan. > I have modelled the structure of a protein using Modeller and then energy > minimized using gromacs. > Then I used the popc128a bilayer from Tieleman sir's website for inserting > the protein. > I created a bigger bilayer using the genconf command in gromacs. > I was able to minimize the bigger bilayer and then inserted my protein in > the bilayer using the genbox command in gromacs. > I was able to minimize the system. > But when I tried to do an mdrun for few steps restraining the protein I > ended with errors like : > 1) pressure scaling more than 1% > 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger > than the 1-4 table size 1.000 nm > These are ignored for the rest of the simulation. > 3) too many lincs warnings. > 4) Number of grid cells is zero. probably the system and the box collapsed. > > I tried to solve these errors by increasing the tau_p value for pressure > scaling error and higher table-extension value for the 1-4 interaction > warning in the mdp file but nothing is working out. > I have given the mdp files at the end for reference. > Please give me some suggestions as how to continue further. > > For energy minimization: > ------------------------------------ > title = Protein in POPC bilayer > cpp = /usr/bin/cpp > define = -DFLEXIBLE > integrator = steep > nsteps = 50000 > > ; Constrain control > constraints = none > > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 100 > nstvout = 100 > nstfout = 100 > > ; nblist update frequency > nstlist = 10 > > ; ns algorithm > ns_type = grid > rlist = 1 > > ; Method for doing VdW > vdw-type = Cut-off > rvdw = 1 > > ; Method for doing electrostatics > coulombtype = Cut-off > rcoulomb = 1 > > ; Center of mass control > nstcomm = 1 > > ; Periodic boundary conditions > pbc = xyz > > ; Mode for center of mass motion removal > comm-mode = Linear > > ; Energy minimizing stuff > emtol = 2250 > emstep = 0.001 > > > For mdrun using position restraints: > --------------------------------------------------- > title = Protein in POPC > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 5000 ; total 10 ps. > nstcomm = 1 > nstxout = 50 > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > ; Berendsen temperature coupling is on in two groups > Tcoupl = berendsen > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Energy monitoring > energygrps = Protein Non-Protein > ; Pressure coupling is not on > Pcoupl = berendsen > tau_p = 5.0 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > Pcoupl_type = semiisotropic > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > Thanking you, > > Yours sincerely, > Pawan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/00417c68/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 19 Mar 2009 13:52:09 +0800 > From: huifang liu <huifangliu1...@gmail.com> > Subject: [gmx-users] how to get the the force plot after pulling > dynamic simulation using GMX-3.3 > To: gmx-users@gromacs.org > Message-ID: > <e523c6be0903182252i114666bam4bbe591a10a30...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am recently doing a SMD. I think i did it very well. But i don't know how > to get the force plot. Is there some one can give me a suggestion? > Thank you very much. > > Huifang > > -- > Huifang Liu (Ph.D. Student) > School of Pharmacy > Fudan University > > 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) > Shanghai, China, 200032 Cell phone: +86-13764669357 > E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/2f249dff/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 19 Mar 2009 10:06:25 +0100 > From: XAvier Periole <x.peri...@rug.nl> > Subject: Re: [gmx-users] Doubt regarding membrane protein in POPC > bilayer > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <c85dbd34-83cd-4f4c-8a4e-5c4224cb7...@rug.nl> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > It is a bit difficult to guess what is exactly happening. Your > starting structure > seem to be the problem, but your topology could also be partly > responsible. > > One easy thing to do is the decrease your time step to 0.0001 which > would > decrease the chances that your system explodes. > > Also try to work on refining your non-bonded set-up, it looks like you > use > straight and short cut-offs. > > XAvier. > > On Mar 19, 2009, at 6:14 AM, Pawan Kumar wrote: > > > Dear gmx-users, > > > > Greetings from Pawan. > > I have modelled the structure of a protein using Modeller and then > > energy minimized using gromacs. > > Then I used the popc128a bilayer from Tieleman sir's website for > > inserting the protein. > > I created a bigger bilayer using the genconf command in gromacs. > > I was able to minimize the bigger bilayer and then inserted my > > protein in the bilayer using the genbox command in gromacs. > > I was able to minimize the system. > > But when I tried to do an mdrun for few steps restraining the > > protein I ended with errors like : > > 1) pressure scaling more than 1% > > 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is > > larger than the 1-4 table size 1.000 nm > > These are ignored for the rest of the simulation. > > 3) too many lincs warnings. > > 4) Number of grid cells is zero. probably the system and the box > > collapsed. > > > > I tried to solve these errors by increasing the tau_p value for > > pressure scaling error and higher table-extension value for the 1-4 > > interaction warning in the mdp file but nothing is working out. > > I have given the mdp files at the end for reference. > > Please give me some suggestions as how to continue further. > > > > For energy minimization: > > ------------------------------------ > > title = Protein in POPC bilayer > > cpp = /usr/bin/cpp > > define = -DFLEXIBLE > > integrator = steep > > nsteps = 50000 > > > > ; Constrain control > > constraints = none > > > > ; Output frequency for coords (x), velocities (v) and forces (f) > > nstxout = 100 > > nstvout = 100 > > nstfout = 100 > > > > ; nblist update frequency > > nstlist = 10 > > > > ; ns algorithm > > ns_type = grid > > rlist = 1 > > > > ; Method for doing VdW > > vdw-type = Cut-off > > rvdw = 1 > > > > ; Method for doing electrostatics > > coulombtype = Cut-off > > rcoulomb = 1 > > > > ; Center of mass control > > nstcomm = 1 > > > > ; Periodic boundary conditions > > pbc = xyz > > > > ; Mode for center of mass motion removal > > comm-mode = Linear > > > > ; Energy minimizing stuff > > emtol = 2250 > > emstep = 0.001 > > > > > > For mdrun using position restraints: > > --------------------------------------------------- > > title = Protein in POPC > > cpp = /usr/bin/cpp > > constraints = all-bonds > > integrator = md > > dt = 0.002 ; ps ! > > nsteps = 5000 ; total 10 ps. > > nstcomm = 1 > > nstxout = 50 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 10 > > nstenergy = 10 > > nstlist = 10 > > ns_type = grid > > rlist = 1.0 > > rcoulomb = 1.0 > > rvdw = 1.0 > > ; Berendsen temperature coupling is on in two groups > > Tcoupl = berendsen > > tc-grps = Protein Non-Protein > > tau_t = 0.1 0.1 > > ref_t = 300 300 > > ; Energy monitoring > > energygrps = Protein Non-Protein > > ; Pressure coupling is not on > > Pcoupl = berendsen > > tau_p = 5.0 5.0 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > Pcoupl_type = semiisotropic > > ; Generate velocites is on at 300 K. > > gen_vel = yes > > gen_temp = 300.0 > > gen_seed = 173529 > > > > Thanking you, > > > > Yours sincerely, > > Pawan > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.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 > > > > ------------------------------ > > Message: 4 > Date: Thu, 19 Mar 2009 10:23:27 +0100 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] compressibility tensor components, pressure > coupling anisotropic PR, triclinic systems > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <col113-w6c9af5515358eb563a4798e...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi, > > If you have a liquid system (no off-diagonal elasticity), you should not > use full anistropic pressure coupling. > If you have a solid system (for instance a crystal), you will have an > elastic shear stress response > and you can determine and use off-diagonal compressibility values. > > You need the compressibility values to set the time scale of the pressure > coupling. > The compressibility does not affect any thermodynamic quantity, only the > dynamics. > The compressibility always occurs as a product with 1/tau_p. > If you want to determine them from a simulation, you need a reasonable > initial guess > for the compressibility and you can use a large tau_p to be on the safe > side > with the actual coupling time. > > Berk > > Date: Wed, 18 Mar 2009 16:02:38 -0700 > From: lastexile...@yahoo.de > To: gmx-users@gromacs.org > Subject: [gmx-users] compressibility tensor components, pressure coupling > anisotropic PR, triclinic systems > > Hello, > > Searching first the gromacs mailing list I could not find an answer to the > problem I face. > > I would like to know the vaules I have to give to the mdp file where it > asks for compressibility. > I have to conduct an NPT simulation using barostat Parrinello-Rahman. My > pressure coupling should be anisotropic. The values I have given up to now > are: > tau_p = 1.0 > compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 > > when I try to calculate the elastic constants I get reasonable values for > the diagonal elements, yet not > good for the off-diagonal. The system I have is a monoclinic one, so > giving zeros to xy,xz,yz components is not an option. > An experimental linear compressibility value I have found out is very close > to the value above, so this is why I think I get good values in the diagonal > elements. > > I have found out many different questions, including one about monoclinic > systems. In one of them someone was wondering why he had to put as input the > compressibility values, while he is supposed to calculate them from the > simulation. As far as the monoclinic system is concerned the question had to > to with the components in gromacs derived from the linear experimental > values.. There was no answer to that. > > I have tried some different values myself, for the off - diagonal > components and I get either a crash of my simulation of different results > for the elastic constants. Is there an algorithm which clearly can point me > to the right direction on how to derive > the right values? > > Thank you in advance, > Nikos > > > > _________________________________________________________________ > What can you do with the new Windows Live? Find out > http://www.microsoft.com/windows/windowslive/default.aspx > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/37a90a04/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 59, Issue 134 > ****************************************** >
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