Dear Rajesh and Damas, Thank you for your help. I will try now. Thanks again. Sincerely, Anh
-----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of gmx-users-requ...@gromacs.org Sent: Thursday, June 20, 2013 10:19 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 110, Issue 115 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.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. Re: Decouple (Justin Lemkul) 2. Re: Test Particle Insertion (Jo?o M. Damas) 3. Re: Decouple (Justin Lemkul) 4. (no subject) (Hari Pandey) 5. Re: (no subject) (Justin Lemkul) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Jun 2013 17:16:29 -0400 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Decouple To: Hari Pandey <hariche...@yahoo.com>, Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <51c3712d.5030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 6/20/13 5:01 PM, Hari Pandey wrote: > Hi , > > How do I solve this problem in GROMACS: > > I have a system with 3 part A,B and C > > I have to put thermostat for A and C but not for B. > Gromacs display error, what is temperature for B. > > > How do aI decouple part B > Per the manual: "tau-t: [ps] time constant for coupling (one for each group in tc-grps), -1 means no temperature coupling" -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 2 Date: Fri, 21 Jun 2013 00:29:15 +0100 From: Jo?o M. Damas <jmda...@itqb.unl.pt> Subject: Re: [gmx-users] Test Particle Insertion To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CAN8VxHxcUPN6Q0fTjRURD0e0vjzP-2uzqODBL_NhHLDdt=4...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Anh, You need to construct a .tpr file for the mdrun -rerun with: - a .gro file with the ligand to be inserted at the end, which _must_ be geometrically centered at 0,0,0 ; - a matching .top file (which means with the ligand topology appropriately inserted) ; - a .mdp file with the specific parameters for the tpi algorithm . Since you happen to have a single particle to insert, that particle's coordinates should be 0,0,0 in the .gro file from grompp (your initial.gro). Best, Jo?o On Thu, Jun 20, 2013 at 8:08 PM, Phan, Anh T. <anhp...@ou.edu> wrote: > Dear GMX Users, > My name is Anh Phan, a PhD student at University of Oklahoma. > I would like to calculate excess chemical potential of one gas > molecule in water solvent using Widom test particle insertion with Gromacs. > In this method, I will insert this gas molecule at a random position > in each configuration of the system. > With Gromacs, I see I can use tpi (integrator = tpi). > I know I have to add this gas molecule in the topology (topol.top) > Also, it is indicated in the manual that insertions are performed > nsteps times in each frame at random locations and with random > orientiations of the molecule. That is what I desire. > The question I would like to ask is whether I have to add the > specified coordinate of gas molecule in the .gro file at the beginning > of running simulation. > For example, in the initial.gro file > ..... > 26734SOL OW45744 21.969 6.237 2.921 > 26734SOL HW145745 21.969 6.253 3.019 > 26734SOL HW245746 21.886 6.188 2.895 > 26735SOL OW45747 15.155 7.211 2.853 > 26735SOL HW145748 15.220 7.265 2.801 > 26735SOL HW245749 15.204 7.151 2.916 > 26736SOL OW45750 24.606 4.896 3.053 > 26736SOL HW145751 24.594 4.972 2.989 > 26736SOL HW245752 24.532 4.896 3.120 > 26737INS X45752 1.000 1.000 1.000 ( Do I > have to add this line in the initial.gro file) > > The command lines > grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o > tpi.tpr -maxwarn 2 mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c > final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid > tpid.xvg > > I am looking forward to receiving your reply. > Thank you for your help. > Sincerely, > Anh > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Jo?o M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ------------------------------ Message: 3 Date: Thu, 20 Jun 2013 21:30:29 -0400 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Decouple To: Hari Pandey <hariche...@yahoo.com>, Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <51c3acb5.4010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Please keep the discussion on the gmx-users mailing list; I am not a private tutor. Comments embedded below. On 6/20/13 8:35 PM, Hari Pandey wrote: > Hi Justin, > Thanks for last help. > > I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of > system, A, B and C. > I want to put thermostat on A and C and couple the tempereture and do not put > any thermostat on B. > > What I want is: after some ps, temperature of A and C should be constant (i.e > reach up to steady state) and B may not be. > > for that My NVT.mdp is: > ; simulation at 300K and 2 ps is on > constraints =all-bonds > integrator =md > dt =0.001 ; ps > nsteps =100000 ; total 100 ps > nstcomm =10 > nstxout =1000 > nstxtcout =0 > nstvout =0 > nstfout =0 > nstenergy =100 > nstlist =100 This value of nstlist is much too large. > ns_type =grid > rlist =0.5 > coulombtype =pme > rcoulomb =0.5 > vdwtype =cut-off > rvdw =0.5 Unless you are using some custom force field that requires 0.5-nm cutoffs, these values are incorrect. > pme_order =4 > ewald_rtol =1e-5 > optimize_fft =yes > DispCorr =no > > ;Brendsen tempereture coupling is on > Tcoupl = nose-hoover Nose-Hoover is a poor choice for initial equilibration, especially when generating velocities. > tau_t =0.001 -1 0.001 Setting tau_t = dt is a bad idea and grompp should have warned you about this. > tc-grps =A B C > > ref_t =750 300 350 > > > ;pressure coupling is on > Pcoupl =no > Pcoupltype =isotropic > tau_p =0.5 > compressibility =1e-5 > ref_p =0.5 > ;generate velocities at 300 k i.e. at room tempereture > gen_vel =yes > gen_temp =750 300 350 > gen_seed =-1 > > MY NPT.mdp is: > > ( here all output control parameters also) > > ;Brendsen tempereture coupling is on > Tcoupl =nose-hoover > tau_t =1 -1 1 > tc-grps =NCALPHA MIDDLE NCNN > ref_t =750 300 350 > > > > ;pressure coupling is on > Pcoupl =Berendsen > Pcoupltype =isotropic > tau_p =0.5 > compressibility =1e-5 > ref_p =1 > ;generate velocities at 300 k i.e. at room tempereture > gen_vel =no > gen_temp =750 300 350 > gen_seed =-1 > > MY NVE.mdp is: > ( here all output control parameters also) > tc-grps = A B C > ref_t =750 300 300 > energygrps = NCALPHA MIDDLE NCNN > tcoupl = nose-hoover > tau-t = 1 -1 1 If you're using thermostats, you're not simulating in an NVE ensemble. > ;pressure coupling is on > Pcoupl =no > ;Pcoupltype =isotropic > ;tau_p =0.5 > ;compressibility =1e-5 > ;ref_p =0.5 > ;generate velocities at 300 k i.e. at room tempereture > gen_vel =no > ; gen_temp =750 300 350 > ; gen_seed =-1 > > > What I did is: > > pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; > editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; > grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; > mdrun -deffnm em -v; > grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; > mdrun -deffnm nvt -v; > grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; > mdrun -deffnm npt -v > grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; > mdrun -deffnm nve -v; > > g_energy -f nve.edr -s nve.tpr -o F1.xvg > > > But the system do not get equilibrated and A, B has not steady state > temperature after time > even 100 ps. please help me, where I did wrong > You have numerous issues, listed above. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 4 Date: Thu, 20 Jun 2013 20:11:28 -0700 (PDT) From: Hari Pandey <hariche...@yahoo.com> Subject: [gmx-users] (no subject) To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> Message-ID: <1371784288.83241.yahoomail...@web163006.mail.bf1.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Hi all? gromacs users I have following (NVT.mdp) (NPT.mdp)? and (NVE.mdp)?? .? I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps,? temperature of A and C should be constant (i.e reach up to steady state) and? B may not be. for that My NVT.mdp is: ; simulation at 300K and 2 ps is on ??????? constraints???? =all-bonds ??????? integrator????? =md ??????? dt????????????? =0.001 ; ps ??????? nsteps????????? =100000 ; total 100 ps ??????? nstcomm???????? =10 ??????? nstxout???????? =1000 ??????? nstxtcout?????? =0 ??????? nstvout???????? =0 ??????? nstfout???????? =0 ??????? nstenergy?????? =100 ??????? nstlist???????? =100 ??????? ns_type???????? =grid ??????? rlist?????????? =0.5 ??????? coulombtype???? =pme ??????? rcoulomb??????? =0.5 ??????? vdwtype???????? =cut-off ??????? rvdw??????????? =0.5 ??????? pme_order?????? =4 ??????? ewald_rtol????? =1e-5 ??????? optimize_fft??? =yes ??????? DispCorr??????? =no ;Brendsen tempereture coupling is on ??????? Tcoupl????????? = nose-hoover ??????? tau_t?????????? =0.001? -1?? 0.001 ??????? tc-grps???????? =A? B ? C ??????? ref_t?????????? =750????? 300?????? 350 ;pressure coupling is on ??????? Pcoupl????????? =no ??????? Pcoupltype????? =isotropic ??????? tau_p?????????? =0.5 ??????? compressibility =1e-5 ??????? ref_p?????????? =0.5 ;generate velocities at 300 k i.e. at room tempereture ??????? gen_vel???????? =yes ??????? gen_temp??????? =750? 300? 350 ??????? gen_seed??????? =-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on ??????? Tcoupl????????? =nose-hoover ??????? tau_t?????????? =1? -1?? 1 ??????? tc-grps???????? =NCALPHA MIDDLE NCNN ??????? ref_t?????????? =750? 300 350 ;pressure coupling is on ??????? Pcoupl????????? =Berendsen ??????? Pcoupltype????? =isotropic ??????? tau_p?????????? =0.5 ??????? compressibility =1e-5 ??????? ref_p?????????? =1 ;generate velocities at 300 k i.e. at room tempereture ??????? gen_vel???????? =no ??????? gen_temp??????? =750 300 350 ??????? gen_seed??????? =-1 MY NVE.mdp is: ( here all output control parameters also) ? tc-grps???????? = A? B? C ??????? ref_t?????????? =750 300 300 ??????? energygrps????? = NCALPHA? MIDDLE? NCNN ??????? tcoupl???????? = nose-hoover ??????? tau-t????????? = 1? -1?? 1 ;pressure coupling is on ??????? Pcoupl????????? =no ??????? ;Pcoupltype????? =isotropic ??????? ;tau_p?????????? =0.5 ??????? ;compressibility =1e-5 ??????? ;ref_p?????????? =0.5 ;generate velocities at 300 k i.e. at room tempereture ??????? gen_vel???????? =no ????? ;? gen_temp??????? =750? 300? 350 ?????? ; gen_seed??????? =-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p? fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm? em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx? -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx? -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx? -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg But the system do not get equilibrated and A, B has not steady state temperature? after?? time ?even 100 ps. please help me, where I did wrong Thanks for your help ________________________________ ------------------------------ Message: 5 Date: Thu, 20 Jun 2013 23:18:07 -0400 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] (no subject) To: Hari Pandey <hariche...@yahoo.com>, Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <51c3c5ef.1010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 6/20/13 11:11 PM, Hari Pandey wrote: > Hi all gromacs users > > I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts > of system, A, B and C. > I want to put thermostat on A and C and couple the tempereture and do not put > any thermostat on B. > > What I want is: after some ps, temperature of A and C should be constant > (i.e reach up to steady state) and B may not be. > > for that My NVT.mdp is: > ; simulation at 300K and 2 ps is on > constraints =all-bonds > integrator =md > dt =0.001 ; ps > nsteps =100000 ; total 100 ps > nstcomm =10 > nstxout =1000 > nstxtcout =0 > > nstvout =0 > nstfout =0 > nstenergy =100 > nstlist =100 > ns_type =grid > rlist =0.5 > coulombtype =pme > rcoulomb =0.5 > vdwtype =cut-off > > rvdw =0.5 > pme_order =4 > ewald_rtol =1e-5 > optimize_fft =yes > DispCorr =no > > > ;Brendsen tempereture coupling is on > Tcoupl = nose-hoover > tau_t =0.001 > -1 0.001 > tc-grps =A B C > > ref_t =750 300 350 > > > ;pressure coupling is on > Pcoupl =no > Pcoupltype =isotropic > tau_p =0.5 > compressibility =1e-5 > ref_p =0.5 > ;generate velocities at 300 k i.e. at room > tempereture > gen_vel =yes > gen_temp =750 300 350 > gen_seed =-1 > > MY NPT.mdp is: > > ( here all output control parameters also) > > > ;Brendsen tempereture coupling is on > Tcoupl =nose-hoover > tau_t =1 -1 1 > tc-grps > =NCALPHA MIDDLE NCNN > ref_t =750 300 350 > > > > ;pressure coupling is on > Pcoupl =Berendsen > Pcoupltype =isotropic > tau_p =0.5 > compressibility =1e-5 > ref_p =1 > ;generate velocities at 300 k i.e. at room tempereture > gen_vel =no > > gen_temp =750 300 350 > gen_seed =-1 > > MY NVE.mdp is: > ( here all output control parameters also) > tc-grps = A B C > > ref_t =750 300 300 > energygrps = NCALPHA MIDDLE NCNN > tcoupl = nose-hoover > tau-t = 1 -1 1 > ;pressure coupling is on > Pcoupl =no > ;Pcoupltype =isotropic > ;tau_p =0.5 > ;compressibility =1e-5 > > ;ref_p =0.5 > ;generate velocities at 300 k i.e. at room tempereture > gen_vel =no > ; gen_temp =750 300 350 > ; gen_seed =-1 > > > > What I did is: > > pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; > editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; > grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; > mdrun -deffnm em -v; > grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; > mdrun -deffnm nvt -v; > grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; > mdrun -deffnm npt -v > grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; > mdrun -deffnm nve -v; > > g_energy -f nve.edr -s nve.tpr -o F1.xvg > > > > But the system do not get equilibrated and A, B has not steady state > temperature after time > even 100 ps. please help me, where I did wrong > See my previous reply: http://lists.gromacs.org/pipermail/gmx-users/2013-June/082392.html -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ -- 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/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 110, Issue 115 ******************************************* -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
