Hi Xavier sir,<br><br>Thanks for your valuable reply.<br>How can I refine the non-bonded set-up ?<br>And where can I specify the time step to 0.0001 ?<br>I am new to gromacs.<br>Sorry to ask such questions.<br><br>Thanking you,<br>
Pawan<br><br><br><div class="gmail_quote">On Thu, Mar 19, 2009 at 2:54 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Doubt regarding membrane protein in POPC bilayer (Pawan Kumar)<br>
2. how to get the the force plot after pulling dynamic<br>
simulation using GMX-3.3 (huifang liu)<br>
3. Re: Doubt regarding membrane protein in POPC bilayer<br>
(XAvier Periole)<br>
4. RE: compressibility tensor components, pressure coupling<br>
anisotropic PR, triclinic systems (Berk Hess)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 19 Mar 2009 10:44:44 +0530<br>
From: Pawan Kumar <<a href="mailto:pawan.chinari@gmail.com">pawan.chinari@gmail.com</a>><br>
Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:143b0c640903182214n2a603f97q478bfac66f502d3e@mail.gmail.com">143b0c640903182214n2a603f97q478bfac66f502d3e@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear gmx-users,<br>
<br>
Greetings from Pawan.<br>
I have modelled the structure of a protein using Modeller and then energy<br>
minimized using gromacs.<br>
Then I used the popc128a bilayer from Tieleman sir's website for inserting<br>
the protein.<br>
I created a bigger bilayer using the genconf command in gromacs.<br>
I was able to minimize the bigger bilayer and then inserted my protein in<br>
the bilayer using the genbox command in gromacs.<br>
I was able to minimize the system.<br>
But when I tried to do an mdrun for few steps restraining the protein I<br>
ended with errors like :<br>
1) pressure scaling more than 1%<br>
2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger<br>
than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation.<br>
3) too many lincs warnings.<br>
4) Number of grid cells is zero. probably the system and the box collapsed.<br>
<br>
I tried to solve these errors by increasing the tau_p value for pressure<br>
scaling error and higher table-extension value for the 1-4 interaction<br>
warning in the mdp file but nothing is working out.<br>
I have given the mdp files at the end for reference.<br>
Please give me some suggestions as how to continue further.<br>
<br>
For energy minimization:<br>
------------------------------------<br>
title = Protein in POPC bilayer<br>
cpp = /usr/bin/cpp<br>
define = -DFLEXIBLE<br>
integrator = steep<br>
nsteps = 50000<br>
<br>
; Constrain control<br>
constraints = none<br>
<br>
; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 100<br>
nstvout = 100<br>
nstfout = 100<br>
<br>
; nblist update frequency<br>
nstlist = 10<br>
<br>
; ns algorithm<br>
ns_type = grid<br>
rlist = 1<br>
<br>
; Method for doing VdW<br>
vdw-type = Cut-off<br>
rvdw = 1<br>
<br>
; Method for doing electrostatics<br>
coulombtype = Cut-off<br>
rcoulomb = 1<br>
<br>
; Center of mass control<br>
nstcomm = 1<br>
<br>
; Periodic boundary conditions<br>
pbc = xyz<br>
<br>
; Mode for center of mass motion removal<br>
comm-mode = Linear<br>
<br>
; Energy minimizing stuff<br>
emtol = 2250<br>
emstep = 0.001<br>
<br>
<br>
For mdrun using position restraints:<br>
---------------------------------------------------<br>
title = Protein in POPC<br>
cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 5000 ; total 10 ps.<br>
nstcomm = 1<br>
nstxout = 50<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.0<br>
rvdw = 1.0<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc-grps = Protein Non-Protein<br>
tau_t = 0.1 0.1<br>
ref_t = 300 300<br>
; Energy monitoring<br>
energygrps = Protein Non-Protein<br>
; Pressure coupling is not on<br>
Pcoupl = berendsen<br>
tau_p = 5.0 5.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0<br>
Pcoupl_type = semiisotropic<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
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<br>
Message: 2<br>
Date: Thu, 19 Mar 2009 13:52:09 +0800<br>
From: huifang liu <<a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a>><br>
Subject: [gmx-users] how to get the the force plot after pulling<br>
dynamic simulation using GMX-3.3<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:e523c6be0903182252i114666bam4bbe591a10a30677@mail.gmail.com">e523c6be0903182252i114666bam4bbe591a10a30677@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
I am recently doing a SMD. I think i did it very well. But i don't know how<br>
to get the force plot. Is there some one can give me a suggestion?<br>
Thank you very much.<br>
<br>
Huifang<br>
<br>
--<br>
Huifang Liu (Ph.D. Student)<br>
School of Pharmacy<br>
Fudan University<br>
<br>
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)<br>
Shanghai, China, 200032 Cell phone: +86-13764669357<br>
E-mail: <a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a> Fax: (86-21)54237264<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 19 Mar 2009 10:06:25 +0100<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] Doubt regarding membrane protein in POPC<br>
bilayer<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:C85DBD34-83CD-4F4C-8A4E-5C4224CB7107@rug.nl">C85DBD34-83CD-4F4C-8A4E-5C4224CB7107@rug.nl</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
<br>
It is a bit difficult to guess what is exactly happening. Your<br>
starting structure<br>
seem to be the problem, but your topology could also be partly<br>
responsible.<br>
<br>
One easy thing to do is the decrease your time step to 0.0001 which<br>
would<br>
decrease the chances that your system explodes.<br>
<br>
Also try to work on refining your non-bonded set-up, it looks like you<br>
use<br>
straight and short cut-offs.<br>
<br>
XAvier.<br>
<br>
On Mar 19, 2009, at 6:14 AM, Pawan Kumar wrote:<br>
<br>
> Dear gmx-users,<br>
><br>
> Greetings from Pawan.<br>
> I have modelled the structure of a protein using Modeller and then<br>
> energy minimized using gromacs.<br>
> Then I used the popc128a bilayer from Tieleman sir's website for<br>
> inserting the protein.<br>
> I created a bigger bilayer using the genconf command in gromacs.<br>
> I was able to minimize the bigger bilayer and then inserted my<br>
> protein in the bilayer using the genbox command in gromacs.<br>
> I was able to minimize the system.<br>
> But when I tried to do an mdrun for few steps restraining the<br>
> protein I ended with errors like :<br>
> 1) pressure scaling more than 1%<br>
> 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is<br>
> larger than the 1-4 table size 1.000 nm<br>
> These are ignored for the rest of the simulation.<br>
> 3) too many lincs warnings.<br>
> 4) Number of grid cells is zero. probably the system and the box<br>
> collapsed.<br>
><br>
> I tried to solve these errors by increasing the tau_p value for<br>
> pressure scaling error and higher table-extension value for the 1-4<br>
> interaction warning in the mdp file but nothing is working out.<br>
> I have given the mdp files at the end for reference.<br>
> Please give me some suggestions as how to continue further.<br>
><br>
> For energy minimization:<br>
> ------------------------------------<br>
> title = Protein in POPC bilayer<br>
> cpp = /usr/bin/cpp<br>
> define = -DFLEXIBLE<br>
> integrator = steep<br>
> nsteps = 50000<br>
><br>
> ; Constrain control<br>
> constraints = none<br>
><br>
> ; Output frequency for coords (x), velocities (v) and forces (f)<br>
> nstxout = 100<br>
> nstvout = 100<br>
> nstfout = 100<br>
><br>
> ; nblist update frequency<br>
> nstlist = 10<br>
><br>
> ; ns algorithm<br>
> ns_type = grid<br>
> rlist = 1<br>
><br>
> ; Method for doing VdW<br>
> vdw-type = Cut-off<br>
> rvdw = 1<br>
><br>
> ; Method for doing electrostatics<br>
> coulombtype = Cut-off<br>
> rcoulomb = 1<br>
><br>
> ; Center of mass control<br>
> nstcomm = 1<br>
><br>
> ; Periodic boundary conditions<br>
> pbc = xyz<br>
><br>
> ; Mode for center of mass motion removal<br>
> comm-mode = Linear<br>
><br>
> ; Energy minimizing stuff<br>
> emtol = 2250<br>
> emstep = 0.001<br>
><br>
><br>
> For mdrun using position restraints:<br>
> ---------------------------------------------------<br>
> title = Protein in POPC<br>
> cpp = /usr/bin/cpp<br>
> constraints = all-bonds<br>
> integrator = md<br>
> dt = 0.002 ; ps !<br>
> nsteps = 5000 ; total 10 ps.<br>
> nstcomm = 1<br>
> nstxout = 50<br>
> nstvout = 1000<br>
> nstfout = 0<br>
> nstlog = 10<br>
> nstenergy = 10<br>
> nstlist = 10<br>
> ns_type = grid<br>
> rlist = 1.0<br>
> rcoulomb = 1.0<br>
> rvdw = 1.0<br>
> ; Berendsen temperature coupling is on in two groups<br>
> Tcoupl = berendsen<br>
> tc-grps = Protein Non-Protein<br>
> tau_t = 0.1 0.1<br>
> ref_t = 300 300<br>
> ; Energy monitoring<br>
> energygrps = Protein Non-Protein<br>
> ; Pressure coupling is not on<br>
> Pcoupl = berendsen<br>
> tau_p = 5.0 5.0<br>
> compressibility = 4.5e-5 4.5e-5<br>
> ref_p = 1.0 1.0<br>
> Pcoupl_type = semiisotropic<br>
> ; Generate velocites is on at 300 K.<br>
> gen_vel = yes<br>
> gen_temp = 300.0<br>
> gen_seed = 173529<br>
><br>
> Thanking you,<br>
><br>
> Yours sincerely,<br>
> Pawan<br>
> _______________________________________________<br>
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<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 19 Mar 2009 10:23:27 +0100<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] compressibility tensor components, pressure<br>
coupling anisotropic PR, triclinic systems<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL113-W6C9AF5515358EB563A4798E960@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
<br>
<br>
<br>
Hi,<br>
<br>
If you have a liquid system (no off-diagonal elasticity), you should not use full anistropic pressure coupling.<br>
If you have a solid system (for instance a crystal), you will have an elastic shear stress response<br>
and you can determine and use off-diagonal compressibility values.<br>
<br>
You need the compressibility values to set the time scale of the pressure coupling.<br>
The compressibility does not affect any thermodynamic quantity, only the dynamics.<br>
The compressibility always occurs as a product with 1/tau_p.<br>
If you want to determine them from a simulation, you need a reasonable initial guess<br>
for the compressibility and you can use a large tau_p to be on the safe side<br>
with the actual coupling time.<br>
<br>
Berk<br>
<br>
Date: Wed, 18 Mar 2009 16:02:38 -0700<br>
From: <a href="mailto:lastexile7gr@yahoo.de">lastexile7gr@yahoo.de</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems<br>
<br>
Hello,<br>
<br>
Searching first the gromacs mailing list I could not find an answer to the problem I face.<br>
<br>
I would like to know the vaules I have to give to the mdp file where it asks for compressibility.<br>
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:<br>
tau_p = 1.0<br>
compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0<br>
<br>
when I try to calculate the elastic constants I get reasonable values for the diagonal elements, yet not<br>
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.<br>
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.<br>
<br>
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.<br>
<br>
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<br>
the right values?<br>
<br>
Thank you in advance,<br>
Nikos<br>
<br>
<br>
<br>
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End of gmx-users Digest, Vol 59, Issue 134<br>
******************************************<br>
</blockquote></div><br>