[gmx-users] RE: Test Particle Insertion
Phan, Anh T.
anhphan at ou.edu
Fri Jun 21 17:28:28 CEST 2013
Dear Rajesh and Damas,
Thank you for your help.
I will try now.
Thanks again.
Sincerely,
Anh
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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 <jalemkul at vt.edu>
Subject: Re: [gmx-users] Decouple
To: Hari Pandey <harichem12 at yahoo.com>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Message-ID: <51C3712D.5030009 at 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 <jmdamas at itqb.unl.pt>
Subject: Re: [gmx-users] Test Particle Insertion
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAN8VxHxcUPN6Q0fTjRURD0e0vjzP-2uzqODBL_NhHLDdt=4RWQ at 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. <anhphan at 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 at gromacs.org
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>
--
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 <jalemkul at vt.edu>
Subject: Re: [gmx-users] Decouple
To: Hari Pandey <harichem12 at yahoo.com>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Message-ID: <51C3ACB5.4010202 at 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 <harichem12 at yahoo.com>
Subject: [gmx-users] (no subject)
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<1371784288.83241.YahooMailNeo at 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 <jalemkul at vt.edu>
Subject: Re: [gmx-users] (no subject)
To: Hari Pandey <harichem12 at yahoo.com>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Message-ID: <51C3C5EF.1010703 at 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
========================================
------------------------------
--
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