[gmx-users] Potein-protein complex simulations

[pawan raghav]

Dear users,
  I am using gromacs to understand the protein-protein
complex interaction stability prediction. for this I have used
protein-protein docked complex as initial .pdb file to simulate. According
to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file needed as input
for drug molecule as seperate from protein file. So please tell me is
this compulsory to use small molecule as seperate, or can I perform MD
simulation by taking complex structure as directly. I am little confuse
about to do this because if I choose this then problem will occurs with
calculating the g_hbond. the g_hbond analyze the H-bonds between the complex
and with complex only. But I am intrested to calculate the H-bonds between
the protein (receptor) and and protein (ligand). Please notify me how can I
make this possible if no then tell me how to make .itp file of protein
(ligand) without using PRODRUG2 SERVER. Because prodrug server produced the
.itp file other than default amino acids example DRG.
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Re: [gmx-users] Potein-protein complex simulations

[Mark Abraham]

On 8/04/2010 5:01 PM, pawan raghav wrote:

Dear users,
   I am using gromacs to understand the protein-protein
complex interaction stability prediction. for this I have used
protein-protein docked complex as initial .pdb file to simulate.
According to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file
needed as input for drug molecule as seperate from protein file. So
please tell me is this compulsory to use small molecule as seperate, or
can I perform MD simulation by taking complex structure as directly. I


You need a topology for the whole system. It may be convenient to 
generate the different [ moleculetype ] sections in different files and 
#include them, or not. What's best depends on your sources of molecule 
topologies.



am little confuse about to do this because if I choose this then
problem will occurs with calculating the g_hbond. the g_hbond analyze


No, such issues are unrelated. g_hbond doesn't care about molecules, it 
just looks for atomic contacts that occur between the sets you specified 
with the index groups.



the H-bonds between the complex and with complex only. But I am
intrested to calculate the H-bonds between the protein (receptor)
and and protein (ligand). Please notify me how can I make this possible


Read g_hbond -h and think about constructing suitable index groups to 
use for this.



if no then tell me how to make .itp file of protein (ligand) without
using PRODRUG2 SERVER. Because prodrug server produced the .itp file
other than default amino acids example DRG.


Mark
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[gmx-users] Re: gmx-users Digest, Vol 72, Issue 36

[Ozge Engin]

ot;utf-8"
>
> Hii Everybody...
>
>
>
> I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
> length and 4-5 molecules wide just as to mimic a rigid metal slab for
> further interaction studies. Can gromacs library support this and how I
> can do that...
>
> All suggestions are welcome.
>
>
>
> Thanks
>
>
>
> Radhika
>
>
>
> Send free SMS to your Friends on Mobile from your Yahoo! Messenger.
> Download Now! http://messenger.yahoo.com/download.php
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100408/4e834c1c/attachment-0001.html
>
> --
>
> Message: 3
> Date: Thu, 08 Apr 2010 15:54:24 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] Simulating a metal slab
> To: Discussion list for GROMACS users 
> Message-ID: <4bbd6f90.7080...@anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 8/04/2010 3:47 PM, radhika jaswal wrote:
> > Hii Everybody...
> >
> > I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
> > length and 4-5 molecules wide just as to mimic a rigid metal slab for
> > further interaction studies. Can gromacs library support this and how I
> > can do that...
>
> Yes, in principle. You will need a force field that supports such
> interactions, and GROMACS does not come with any. Your first place to
> look should be in the published literature for other simulations of such
> materials and such slabs. Don't assume GROMACS is the best tool for the
> task.
>
> Mark
>
>
> --
>
> Message: 4
> Date: Thu, 8 Apr 2010 11:27:37 +0530
> From: shahid nayeem 
> Subject: Re: [gmx-users] position_restraint anfd full Dynamics and
>berendsen   Nose hoover Thermostat
> To: Discussion list for GROMACS users 
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Please see the following pr.mdp and full.mdp
> pr.mdp
>
>
> cpp = /usr/bin/cpp
>
> define = -DPOSRES
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 5 ; total 100 ps.
>
> nstcomm = 1
>
> nstxout = 500
>
> 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 = ProteinNon-protein
>
> tau_t = 0.1  0.1
>
> ref_t = 500 500
>
> ; Energy monitoring
>
> energygrps = Protein Non-protein
>
> ; Pressure coupling is not on
>
> Pcoupl = no
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is on at 500 K.
>
> gen_vel = yes
>
> gen_temp = 500.0
>
> gen_seed = 173529
>
> full.mdp
>
> cpp = /usr/bin/cpp
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 5000 ; total 10 ps.
>
> nstcomm = 1
>
> nstxout = 5000
>
> nstvout = 4
>
> nstfout = 0
>
> nstlog = 100
>
> nstenergy = 100
>
> 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 = 0.10.1
>
> ref_t = 500 500
>
> ; Energy monitoring
>
> energygrps = Protein Non-protein
>
> ; Isotropic pressure coupling is now on
>
> Pcoupl = berendsen
>
> Pcoupltype = isotropic
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is off at 500 K.
>
> gen_vel = no
>
> gen_temp = 500.0
>
> gen_seed = 173529
>
> Please tell me why protein shows unfolding in very first frame.
>
> msnayeem
>
>
>
>
>
>
>
> On 4/7/10, Mark Abraham  wrote:
> >
> > On 7/04/2010 9:08 PM, shahid nayeem wrote:
> >
> >> Dear users
> >> Please let me know some basic question. I am sorry if I am asking a
> >> silly question.
> >> a) While simulating a protein thermal unfolding at high temperature say
> >> 500K should I run position restraint dynamics at 500k or at 298K. I am
> >> doing 100ps position restraint dynamics at 500k. Am I right in doing so.
> >>
> >
> > The usual purpose of position restrained MD is to allow the system to
> > achie

Re: [gmx-users] Lateral pressure profile in membrane simulations

[Martti Louhivuori]

On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote:
I am doing some molecular dynamics simulations of membrane systems  
and i would like to ask you if someone know or have a code for the  
calculation of the lateral pressure profile  from the data obtained  
doing  membrane simulations.


You can find everything you need from here:
http://www.cgmartini.nl/index.php/tools/114-3d-pf

It is a custom version of Gromacs that calculates a 3D pressure field  
using the -rerun option of mdrun, as explained in Ollila et al. (2009)  
PhysRevLett 102: 078101. Before you do the rerun, you need to redo  
grompp with 'userreal1' set to the desired grid size. The analysis  
tools there can then be used to calculate e.g. a lateral pressure  
profile... Note that constraints are a bit problematic, though, so if  
your lipids have constraints, the profile may not be accurate.


Best regards,
-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398

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Re: [gmx-users] Re: EM crashes

[Mark Abraham]

On 8/04/2010 5:24 PM, Ozge Engin wrote:

Hi Ravi,

I had a similar problem to yours when I was dealing with simulation of a
peptide channel. I had the crystal structure of the channel consisting
of crystal water molecules and the peptide channel. I energy minimized
the system. Although nothing seems to be overlap, energy minimization
crashed. After that I decided to put each water molecule into the
channel one by one, and did energy minimization after each water
molecule. If the energy minimization did not crash, I continued adding
another water molecule. If it crashed I changed the location of the last
water molecule in the channel. But I am afraid you have much more water
molecules than mine. I had more or less 100 water molecules within the
channel, and also note that I had not any ions in the system.


EM can also crash because of voids... if there's a hole, then things 
will tend to fill it, which can lead to a problem elsewhere.


Also, on the ions, consider introducing them after no-ions EM is working 
properly.


Mark
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[gmx-users] install problem of ngmx.

[kecy_wu]

Hello, I installed the gromacs4.0.5, when I made, it had lots of mistakes, 
below is some of the mistakes: 
In file included from ngmx.c:50:
Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory
Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory
Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory
Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory
In file included from ./xutil.h:43,
from ./xdlgitem.h:42,
from xdlg.h:40,
from dialogs.h:40,
from ngmx.c:54:
./x11.h:57: error: expected specifier-qualifier-list before 'Display'
./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent'
./x11.h:79: error: expected declaration specifiers or '...' before 'Window'
./x11.h:82: error: expected specifier-qualifier-list before 'Window'
In file included from ./xdlgitem.h:42,
from xdlg.h:40,
from dialogs.h:40,
from ngmx.c:54:
./xutil.h:49: error: expected specifier-qualifier-list before 'Window'
./xutil.h:57: error: expected ')' before 'win'
./xutil.h:61: error: expected ')' before '*' token
./xutil.h:63: error: expected declaration specifiers or '...' before 
'XFontStruct'
./xutil.h:63: error: expected declaration specifiers or '...' before 'Drawable'
./xutil.h:67: error: expected declaration specifiers or '...' before 'Drawable'
./xutil.h:75: error: expected ')' before '*' token
./xutil.h:77: error: expected ')' before '*' token
./xutil.h:79: error: expected ')' before '*' token
./xutil.h:81: error: expected ')' before '*' token
./xutil.h:84: error: expected ')' before '*' token
./xutil.h:87: error: expected ')' before '*' token
./xutil.h:89: error: expected ')' before '*' token
./xutil.h:91: error: expected ')' before '*' token
In file included from xdlg.h:40,
from dialogs.h:40,
from ngmx.c:54:
./xdlgitem.h:66: error: expected specifier-qualifier-list before 'Pixmap'
./xdlgitem.h:98: error: expected declaration specifiers or '...' before 'XEvent'
./xdlgitem.h:142: error: expected declaration specifiers or '...' before 
'Pixmap'
In file included from dialogs.h:40,
from ngmx.c:54:
xdlg.h:63: error: expected specifier-qualifier-list before 'Window'
xdlg.h:81: error: expected declaration specifiers or '...' before 'Window'
xdlg.h:140: error: expected declaration specifiers or '...' before 'Window'
In file included from pulldown.h:40,
from dialogs.h:41,
from ngmx.c:54:
popup.h:44: error: expected specifier-qualifier-list before 'Window'
popup.h:53: error: expected specifier-qualifier-list before 'Window'
popup.h:58: error: expected specifier-qualifier-list before 'Window'
popup.h:64: error: expected declaration specifiers or '...' before 'Window'
In file included from dialogs.h:41,
from ngmx.c:54:
pulldown.h:51: error: expected declaration specifiers or '...' before 'Window'
In file included from manager.h:45,
from dialogs.h:42,
from ngmx.c:54:
nleg.h:54: error: expected declaration specifiers or '...' before 'Window'
In file included from manager.h:46,
from dialogs.h:42,
from ngmx.c:54:
buttons.h:64: error: expected declaration specifiers or '...' before 'Window'
buttons.h:64: error: expected declaration specifiers or '...' before 'Window'
buttons.h:69: error: expected declaration specifiers or '...' before 'Window'
buttons.h:69: error: expected declaration specifiers or '...' before 'Window'
In file included from dialogs.h:42,
from ngmx.c:54:
manager.h:133: error: expected declaration specifiers or '...' before 'Window'
In file included from dialogs.h:43,
from ngmx.c:54:
logo.h:44: error: expected specifier-qualifier-list before 'XFontStruct'
logo.h:53: error: expected declaration specifiers or '...' before 'Window'
In file included from ngmx.c:57:
nmol.h:43: error: expected declaration specifiers or '...' before 'Window'
ngmx.c:65: error: expected declaration specifiers or '...' before 'Window'
ngmx.c: In function 'dump_xw':
ngmx.c:70: error: 'w' undeclared (first use in this function)
ngmx.c:70: error: (Each undeclared identifier is reported only once
ngmx.c:70: error: for each function it appears in.)
ngmx.c:411: error: 't_x11' has no member named 'bg'
ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer 
without a cast
ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer 
type
ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer 
type
ngmx.c:412: error: too many arguments to function 'init_pd'
make[3]: *** [ngmx.o] Error 1
make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'
make: *** [all-recursive] Error 1
I hope you can give me some suggestions to solve the problom。
Thank you very much!-- 
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Plea

Re: [gmx-users] install problem of ngmx.

[Mark Abraham]

On 8/04/2010 5:52 PM, kecy...@sina.com wrote:


Hello, I installed the gromacs4.0.5, when I made, it had lots of
mistakes, below is some of the mistakes:


You should prefer to install the latest version, not one that's over a 
year old. Bugs get fixed...


Unless you're planning to use ngmx you can use "./configure --without-X" 
and this problem will go away.


configure should really have recognized that ngmx couldn't be compiled. 
If you've not run configure on this machine in the same shell from which 
you try to make, go and do that properly. If you have done this 
properly, then you have something "unique" about your machine...


Mark


/In file included from ngmx.c:50:/

/Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory/

/Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory/

/Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory/

/Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory/

/In file included from ./xutil.h:43,/

/from ./xdlgitem.h:42,/

/from xdlg.h:40,/

/from dialogs.h:40,/

/from ngmx.c:54:/

/./x11.h:57: error: expected specifier-qualifier-list before 'Display'/

/./x11.h:79: error: expected declaration specifiers or '...' before
'XEvent'/

/./x11.h:79: error: expected declaration specifiers or '...' before
'Window'/

/./x11.h:82: error: expected specifier-qualifier-list before 'Window'/

/In file included from ./xdlgitem.h:42,/

/from xdlg.h:40,/

/from dialogs.h:40,/

/from ngmx.c:54:/

/./xutil.h:49: error: expected specifier-qualifier-list before 'Window'/

/./xutil.h:57: error: expected ')' before 'win'/

/./xutil.h:61: error: expected ')' before '*' token/

/./xutil.h:63: error: expected declaration specifiers or '...' before
'XFontStruct'/

/./xutil.h:63: error: expected declaration specifiers or '...' before
'Drawable'/

/./xutil.h:67: error: expected declaration specifiers or '...' before
'Drawable'/

/./xutil.h:75: error: expected ')' before '*' token/

/./xutil.h:77: error: expected ')' before '*' token/

/./xutil.h:79: error: expected ')' before '*' token/

/./xutil.h:81: error: expected ')' before '*' token/

/./xutil.h:84: error: expected ')' before '*' token/

/./xutil.h:87: error: expected ')' before '*' token/

/./xutil.h:89: error: expected ')' before '*' token/

/./xutil.h:91: error: expected ')' before '*' token/

/In file included from xdlg.h:40,/

/from dialogs.h:40,/

/from ngmx.c:54:/

/./xdlgitem.h:66: error: expected specifier-qualifier-list before 'Pixmap'/

/./xdlgitem.h:98: error: expected declaration specifiers or '...' before
'XEvent'/

/./xdlgitem.h:142: error: expected declaration specifiers or '...'
before 'Pixmap'/

/In file included from dialogs.h:40,/

/from ngmx.c:54:/

/xdlg.h:63: error: expected specifier-qualifier-list before 'Window'/

/xdlg.h:81: error: expected declaration specifiers or '...' before 'Window'/

/xdlg.h:140: error: expected declaration specifiers or '...' before
'Window'/

/In file included from pulldown.h:40,/

/from dialogs.h:41,/

/from ngmx.c:54:/

/popup.h:44: error: expected specifier-qualifier-list before 'Window'/

/popup.h:53: error: expected specifier-qualifier-list before 'Window'/

/popup.h:58: error: expected specifier-qualifier-list before 'Window'/

/popup.h:64: error: expected declaration specifiers or '...' before
'Window'/

/In file included from dialogs.h:41,/

/from ngmx.c:54:/

/pulldown.h:51: error: expected declaration specifiers or '...' before
'Window'/

/In file included from manager.h:45,/

/from dialogs.h:42,/

/from ngmx.c:54:/

/nleg.h:54: error: expected declaration specifiers or '...' before 'Window'/

/In file included from manager.h:46,/

/from dialogs.h:42,/

/from ngmx.c:54:/

/buttons.h:64: error: expected declaration specifiers or '...' before
'Window'/

/buttons.h:64: error: expected declaration specifiers or '...' before
'Window'/

/buttons.h:69: error: expected declaration specifiers or '...' before
'Window'/

/buttons.h:69: error: expected declaration specifiers or '...' before
'Window'/

/In file included from dialogs.h:42,/

/from ngmx.c:54:/

/manager.h:133: error: expected declaration specifiers or '...' before
'Window'/

/In file included from dialogs.h:43,/

/from ngmx.c:54:/

/logo.h:44: error: expected specifier-qualifier-list before 'XFontStruct'/

/logo.h:53: error: expected declaration specifiers or '...' before 'Window'/

/In file included from ngmx.c:57:/

/nmol.h:43: error: expected declaration specifiers or '...' before 'Window'/

/ngmx.c:65: error: expected declaration specifiers or '...' before 'Window'/

/ngmx.c: In function 'dump_xw':/

/ngmx.c:70: error: 'w' undeclared (first use in this function)/

/ngmx.c:70: error: (Each undeclared identifier is reported only once/

/ngmx.c:70: error: for each function it appears in.)/

/ngmx.c:411: error: 't_x11' has no member named 'bg'/

/ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from
integer without a cast/

/ngmx.c:412: warning: passing argument 8 of

[gmx-users] H-bonds

[Carla Jamous]

Hi,

please I'm trying to measure an hbond between 2 specific atoms. When I used
g_hbond I didn't the result I expected because it doesn't specify the atoms
that constitute the H bond.
Now I'm trying with g_dist but I encountered a problem: when I do the
following in my index file:

r 172 & a HD2

it tells me: empty group

So please can anyone help me?

Thank you.
Carla
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[gmx-users] g_nmeig_d error

[sarbani chattopadhyay]

Hi,
   I am trying to do normal mode analysis on a protein having 6398 atoms. I 
energy 
minimized the structure using steepest descent followed by L-BFGS minimization 
technique 
. The Fmax was equal to 9.67927896882578e-07.

I then went on to perform normal mode analysis. The command was
nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &

Then ,when I tried to diagonalize the matrix , the command being:
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr

I get the error message as :
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error 
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

I am using a 8 node computer each with a RAM of 2 GB. ( g_nmeig_d runs on a 
single node).
Gromacs has been compiled in 64 bit mode.

I have no clue regarding this problem.
Any suggestion will be of great help.
Thanks in advance.
Sarbani Chattopadhyay-- 
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[gmx-users] Sarath Kumar Baskaran wants to stay in touch on LinkedIn

[Sarath Kumar Baskaran]

LinkedIn
Sarath Kumar Baskaran requested to add you as a connection on 
LinkedIn:
--

Chinmay,

I'd like to add you to my professional network on LinkedIn.

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Re: [gmx-users] Potential Tables for user defined potentials

[sulatha M. S]

Thanks Justin,

I have followed the How- tos/Polymers for creating rtp entries
for polyacrylates/acids and have been able to run MD simulations
successfully reproducing results from prior literature.
Tabulated potentials section is also sure to help gmx-users. Thanks!


Dr. M.S Sulatha
IIT-Madras,
India


On 4/8/10, Justin A. Lemkul  wrote:
>
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Gareth Tribello wrote:
>>
>>> Hello again
>>>
>>> OK I have posted my notes on user defined potnetials here.  I think there
>>> pretty exaustive (well they have everything I know about this in) and could
>>> be used as a how to in this form.  However, I can't work out how to post
>>> them on the webiste as a how to page.
>>>
>>>
>> Great, I'll try to find some time to get a How-To together and post this
>> file as an attachment.  I'll report back when that's done so others can add
>> to it.
>>
>
> OK, I've got this all wikified now, complete with fancy equations :)
>
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>
> Hopefully this information will help de-complicate the issue of tabulated
> potentials, and now that the page is set up, everyone can feel free to add
> and modify to their hearts' content.
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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Re: [gmx-users] H-bonds

[Justin A. Lemkul]

Carla Jamous wrote:

Hi,

please I'm trying to measure an hbond between 2 specific atoms. When I 


You won't be able to.  A hydrogen bond is defined as occurring between 3 atoms 
(D-H...A) for geometric reasons, so you have to specify at least three atoms for 
the analysis.


used g_hbond I didn't the result I expected because it doesn't specify 
the atoms that constitute the H bond.
Now I'm trying with g_dist but I encountered a problem: when I do the 
following in my index file:


r 172 & a HD2

it tells me: empty group



Apparently there is no atom named "HD2" in residue 172.  Be sure you're 
analyzing the right residue.


-Jusitn


So please can anyone help me?

Thank you.
Carla



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Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

Dear Dr. Mark,

Thanks very much for pointing out that GROMACS can handle multiple instances
of the parameters with different n for a single dihedral.

However, given that, in the existing ffamber ports in GROMACS  the other
dihedral parameters have been converted to RB form, would it make a
difference to just import these new parameters in the non-RB form?

To my knowledge, the torsional term should not vary (or, vary within
acceptable limits) irrespective of the functional form used to calculate it.
But I would like to know if there could be some reason for which this
assumption cannot be made.

Dear Dr. Alan,

Thanks very much for pointing out to the acpypi code. I was able to better
understand the conversion procedure.

Sincerely,
Vignesh

On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham wrote:

> On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>
>> Dear Users,
>>
>> I am trying to port the new parmbsc0 forcefield
>> (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
>> simulations.
>>
>> While unit conversions are sufficient to convert many of the parameters
>> from AMBER to GROMACS format, dihedral angle conversion does not seem to
>> be straight forward - the dihedral parameters need to be converted to
>> the Ryckaert-Bellemans parameters.
>>
>
> Why? GROMACS can probably do the non-RB form - IIRC you can implement a sum
> of multiple instances of 4.61 with different n.
>
>
>  I went through the GROMACS 4.0
>> manual, especially equations 4.61-4.65 to understand the procedure. The
>> procedure involves comparing the fourier expansion of the IUPAC
>> convention of dihedral potential (equation 4.65) with the
>> Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
>> to get the Cn's of the RB function. However, I am not able to understand
>> how to account for the phase angles. (Also to note, the parmbsc0
>> forcefield contains phase angles other than 0 and 180.)
>>
>
> Elegant conversion formulae require those angles to be convenient...
>
> Mark
>
>
>   Any advice or suggestion will be of great help.
>>
>> Thank you,
>>
>> Vignesh
>>
>> --
>> R.Vigneshwar
>> Graduate Student,
>> Dept. of Chemical & Biomolecular Engg,
>> National University of Singapore,
>> Singapore
>>
>> "Strive for Excellence, Never be satisfied with the second Best!!"
>>
>> I arise in the morning torn between a desire to improve the world and a
>> desire to enjoy the world. This makes it hard to plan the day. (E.B.
>> White)
>>
>>  --
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-- 
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Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

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Re: [gmx-users] problem with total energy

[jampani srinivas]

Hi

Thanks for your response, I am allowing the two groups (frozen and
non-frozen) groups interact each other, i guess i am getting the energy of
total system from g_energy.

I checked the velocities of frozen group atoms, they are not "zero". I have
seen in git master that this problem was fixed and updated in md.c file, I
have downloaded this from git master and compiled my gromacs again still i
found that frozen atoms gets the initial velocity.

I am not at all clear why the energy of system should blow up, can you
please help me if there is solution for this.

Thanks in advance.

Srinivas.

On Wed, Apr 7, 2010 at 4:47 PM, ms  wrote:

> jampani srinivas ha scritto:
> > Dear Berk,
> >
> > I am sorry if i am confusing you with my poor description of problem,
> > actually I have submitted simulation with two temperature coupling groups
> (i
> > think you already know that from our earlier conversations) and found
> that
> > there is a continuous increase in the total energy of the system. I could
> > not observe any blowing in the output file but the system energy is
> > continuously increasing, i am using 4fs time step here. Can you please
> let
> > me know if i have to give more details?
> >
>
> Which part of the system is increasing its energy?
>
> m.
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[gmx-users] Problem with g_density

[prithvi raj pandey]

Dear gmx-users,

I have generated 40ns trajectories for DPPC bilayer - water system. The
whole 40ns was generated in small trajectories and finally I concatenated
all the small trajectories to a big 40 ns trajectory using the following
options in trjcat

trjcat   -f   -o   -settime   -tu

Now the problem is when I am trying to plot partial density along the
bilayer - water interface axis (i.e. Z) using the big trajectory  for
different groups (e.g., water,DPPC etc.), density for water comes around 150
kg/m^3. But for any of the small trajectories the value is ok (i.e. around
1000). The plots were done using the folloing tool

   g_density   -f-o   -n   -s  -d Z

Can anyone help?



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[gmx-users] xml

[#ZHAO LINA#]

During configuration, there is something about xml.
a functions in analysis
  --without-xml do not link to the xml2 library, disallows the 
use of certain file formats

1. which file formats did they specify to? 
2. Can gromacs handle the PDBML file? 

Thanks and regards,

lina

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Re: [gmx-users] xml

[David van der Spoel]

On 2010-04-08 17.39, #ZHAO LINA# wrote:

During configuration, there is something about xml.
a functions in analysis
   --without-xml do not link to the xml2 library, disallows the 
use of certain file formats

1. which file formats did they specify to?

none.


2. Can gromacs handle the PDBML file?

no.



Thanks and regards,

lina





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Re: [gmx-users] Potein-protein complex simulations

[Lucio Ricardo Montero Valenzuela]

If you are working with a two-protein complex, you don't need PRODRG.
You can create the complex topology in pdb2gmx using as input a PDB file
with two chains, each chain for a protein. Then pdb2gmx does the job of
creating an itp file for each protein, and a top file for the complex,
which has #include statements for the itp files.
Best regards.
Lucio Montero
Dr. Federico Sánchez Lab
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210
Mexico

El jue, 08-04-2010 a las 00:01 -0700, pawan raghav escribió:
> Dear users,
>   I am using gromacs to understand the protein-protein
> complex interaction stability prediction. for this I have used
> protein-protein docked complex as initial .pdb file to simulate.
> According to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file
> needed as input for drug molecule as seperate from protein file. So
> please tell me is this compulsory to use small molecule as seperate,
> or can I perform MD simulation by taking complex structure as
> directly. I am little confuse about to do this because if I choose
> this then problem will occurs with calculating the g_hbond. the
> g_hbond analyze the H-bonds between the complex and with complex only.
> But I am intrested to calculate the H-bonds between the protein
> (receptor) and and protein (ligand). Please notify me how can I make
> this possible if no then tell me how to make .itp file of protein
> (ligand) without using PRODRUG2 SERVER. Because prodrug server
> produced the .itp file other than default amino acids example DRG.
> 
> 
> 
> 
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[gmx-users] InflateGRO and pentamer protein simulation

[xi zhao]

Dear sir :
I want to a pentamer membrane protein, when I used InflateGRO.pl with DOUGHNUT 
Mode, the results were wrong, please help me! 
show " [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 
kk_inflated.gro 5 area.dat doughnut protein_subunits
Doughnut mode activated. Protein coordinates will be translated by subunit 
Reading. 
Reading chain identifiers 
Subunit 1:  atom 1 to  atom 3238 
Subunit 2:  atom 3239 to  atom 6476 
Subunit 3:  atom 6477 to  atom 9714 
Subunit 4:  atom 9715 to  atom 12952 
Subunit 5:  atom 12953 to  atom 16190 
There are 5 protein subunits 
Scaling lipids
There are 512 lipids...
with 65 atoms per lipid..
Determining upper and lower leaflet...
256 lipids in the upper...
256 lipids in the lower leaflet 
Checking for overlap
...this might actually take a while...
...
Argument "N4" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C1" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C2" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C3" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "N4" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708,  line 
5.
Calculating Area per lipid...
Protein X-min/max: 23    105
Protein Y-min/max: 18    100
X-range: 82 A    Y-range: 82 A
Building 82 X 82 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 49 nm^2
Area per lipid: 9.83158146861789 nm^2
Area per protein, upper half: 38.75 nm^2
Area per lipid, upper leaflet : 9.79362516645161 nm^2
Area per protein, lower half: 45.75 nm^2
Area per lipid, lower leaflet : 9.92548787409836 nm^2
Writing Area per lipid...
Done!


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Re: [gmx-users] InflateGRO and pentamer protein simulation

[Justin A. Lemkul]

xi zhao wrote:



Dear sir :
I want to a pentamer membrane protein, when I used InflateGRO.pl with 
/DOUGHNUT Mode, the results were wrong, please help me! /


If you want any useful help, you'll have to do a whole lot better than simply 
saying "the results were wrong."  No one on this list will have any idea what 
you mean.  If you believe there is some error in the script itself, you're 
better off contacting its author.


-Justin

4 
show 
" [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 
14 kk_inflated.gro 5 area.dat doughnut protein_subunits
Doughnut mode activated. Protein coordinates will be translated by 
subunit 

Reading.
Reading chain identifiers
Subunit 1:  atom 1 to  atom 3238
Subunit 2:  atom 3239 to  atom 6476
Subunit 3:  atom 6477 to  atom 9714
Subunit 4:  atom 9715 to  atom 12952
Subunit 5:  atom 12953 to  atom 16190
There are 5 protein subunits
Scaling lipids
There are 512 lipids...
with 65 atoms per lipid..
Determining upper and lower leaflet...
256 lipids in the upper...
256 lipids in the lower leaflet
Checking for overlap
...this might actually take a while...
...
Argument "N4" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C1" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C2" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C3" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "N4" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708, 
 line 5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708, 
 line 5.

Calculating Area per lipid...
Protein X-min/max: 23105
Protein Y-min/max: 18100
X-range: 82 AY-range: 82 A
Building 82 X 82 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 49 nm^2
Area per lipid: 9.83158146861789 nm^2
Area per protein, upper half: 38.75 nm^2
Area per lipid, upper leaflet : 9.79362516645161 nm^2
Area per protein, lower half: 45.75 nm^2
Area per lipid, lower leaflet : 9.92548787409836 nm^2
Writing Area per lipid...
Done!


 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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[gmx-users] Problem with g_density

[chris . neale]

1. Please include the actual commands that you used via copy and paste  
so that we can see *exactly* what you did.


2. Please include a snippit of the *actual* output identifying where  
the difference is that you mention here.


3. Note that g_density has some limitations, all related to volume  
fluctuations:
3a. It doesn't account for volume fluctuations when normalizing the  
counts to get the density (not a problem for NVT):


  for (n =0; n < nr_grps; n++) {
for (i = 0; i < *nslices; i++)
  (*slDensity)[n][i] = (*slDensity)[n][i] * (*nslices) /
( nr_frames * box[axis][axis] * box[ax1][ax1] * box[ax2][ax2]);
  }

3b. Even if you center your bilayer along Z (with this program or with  
trjconv preprocessing), the bilayer center may fluctuate along z  
because bin numbering always starts at the bottom of the box (not a  
problem for NVT):


/* determine which slice atom is in */
slice = (int)(z / (*slWidth));
(*slDensity)[n][slice] += top->atoms.atom[index[n][i]].m;

User-beware.

Chris.

--original message --

Dear gmx-users,

I have generated 40ns trajectories for DPPC bilayer - water system. The
whole 40ns was generated in small trajectories and finally I concatenated
all the small trajectories to a big 40 ns trajectory using the following
options in trjcat

trjcat   -f   -o   -settime   -tu

Now the problem is when I am trying to plot partial density along the
bilayer - water interface axis (i.e. Z) using the big trajectory  for
different groups (e.g., water,DPPC etc.), density for water comes around 150
kg/m^3. But for any of the small trajectories the value is ok (i.e. around
1000). The plots were done using the folloing tool

   g_density   -f-o   -n   -s  -d Z

Can anyone help?


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[gmx-users] Re: Bilayer

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I cannot 
serve as a private tutor, and I do get numerous requests.  You stand a much 
better chance of reaching someone with useful advice by posting to the list.  I 
have a few ideas (see below), so I am CC'ing the list to benefit the community 
and perhaps stimulate further responses.  Archiving your questions and responses 
will help others down the road who have the same issues.  That also reduces my 
personal inbox traffic :)


Clark, Tiffany D wrote:

Hello Mr. Lemkul,

 

I am a graduate student at East Carolina University and I am trying to 
construct a heterogeneous lipid bilayer for use in a md simulation using 
GROMACS.  As I have been searching for help online you have emerged as 
an expert in the field with your ablity to provide the most insight and 
helpful advice.  I am hoping you are willing to share some of your 
knowledge with me.


 

I am trying to create a 4:1 mixture of POPC and POPG respectively.  I 
will be using the Berger lipids force field (lipid parameters by D. 
Peter Tieleman).  I am thinking the best approach maybe to construct a 
set of  lipids (DPOPC, LPOPC, DPOPG and LPOPG) and then propagate that 


There is no need to re-construct any lipids.  Just extract a single lipid 
molecule from the pre-equilibrated bilayers at Tieleman's site.  Don't 
differentiate between different stereoisomers of POPC; the topology provided by 
Tieleman does not pertain to both possible forms.


using GROMACS editconf.  I am struggling with how to get things 


A combination of editconf and genconf would be useful.  You could construct a 
small box with the appropriate lipid ratio, then replicate it with genbox -nbox 
to create a monolayer of sufficient size.  Create a duplicate monolayer and 
rotate it with editconf, concatenate the structures, and presto, you have a 
bilayer.  This structure will of course require substantial equilibration (tens 
to hundreds of ns) due to its artificial regularity.


started.  I  have .itp files for both POPC and POPG (from 
http://moose.bio.ucalgary.ca/index.php?page=Downloads) but how do I 
generate topologies for the new positions of the lipids?  I have noticed 


Topologies and positions are independent.  The only requirement is that the 
[molecules] section of your .top matches the order of the molecules present in 
your coordinate file (aside from the obvious nomenclature of atoms).


that may people have just changed the head group and made small changes 
to the topology file


 

Is the only way to create a GROMACS .top file for a lipid to write it 
yourself?  What is the best way to generated the starting coordinates of 


It should be very straightforward to write the topology, just #include the 
necessary topologies (all of which you already have) within the .top file.


my lipids?  I have constructed each of the lipids and minimized the 
structures (using Amber), though I don’t think this will be useful for 
the construction of the bilayer (in GROMACS).  The .pdb files available 


Probably not.  The AMBER-output structures will likely be all-atom molecules 
with atom naming that has no relationship to the names defined in the 
Tieleman-provided topologies.  See my comment above for a reasonable (and 
extraordinarily easy) method for getting the coordinates of a single lipid.


on Dr. Tieleman’s website are bilayers and not individual lipids (would 
you advise me to start with a lipid structure isolated from one of the 
bilayers?). 



Indeed, yes :)

 

Any advice or recommendations you are willing to share would be most 
appreciated.  None of the faculty here work with GROMACS and I am 
struggling to understand how a bilayer can be constructed based upon 
topology files (.itp) or if only amendments are possible.




Then you've been assigned an unfortunate task.  What you are looking to do is 
fairly complicated for someone who is unfamiliar with GROMACS and without an 
immediate support system you are in for a lot of archive reading and waiting 
around for free help.


What you really need to get comfortable with is the fact that a topology has 
nothing to do with coordinates, thus no structure can be built from a topology. 
 Crafty use of editconf and genconf are all you need to build the system.


Good luck.

-Justin

 


Gratefully yours,

 


Tiffany D. Clark



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Ca

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Mark Abraham]

On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:

Dear Dr. Mark,

Thanks very much for pointing out that GROMACS can handle multiple
instances of the parameters with different n for a single dihedral.


I hope I'm right there. There's been discussion on such topics before. 
There's some subtle difference between [ dihedrals ] and [ dihedraltypes 
] which eludes my memory, but which will be in the archives.



However, given that, in the existing ffamber ports in GROMACS  the other
dihedral parameters have been converted to RB form, would it make a
difference to just import these new parameters in the non-RB form?


It will make no numerical difference, but g_energy will probably report 
the contribution from the two different functional forms separately. 
Attempting to mix *non-bonded* interactions in this kind of way asks for 
trouble, because the maths is not well-defined. Here, you're fine, 
because the maths is right.



To my knowledge, the torsional term should not vary (or, vary within
acceptable limits) irrespective of the functional form used to calculate
it. But I would like to know if there could be some reason for which
this assumption cannot be made.


The R-B form might be more efficient to evaluate than a sum of simple 
dihedrals in the cases where the angle is zero or 180, which might 
explain the ffamber practice.


Mark


Dear Dr. Alan,

Thanks very much for pointing out to the acpypi code. I was able to
better understand the conversion procedure.

Sincerely,
Vignesh

On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote:

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:

Dear Users,

I am trying to port the new parmbsc0 forcefield
(http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the
parameters
from AMBER to GROMACS format, dihedral angle conversion does not
seem to
be straight forward - the dihedral parameters need to be
converted to
the Ryckaert-Bellemans parameters.


Why? GROMACS can probably do the non-RB form - IIRC you can
implement a sum of multiple instances of 4.61 with different n.


I went through the GROMACS 4.0
manual, especially equations 4.61-4.65 to understand the
procedure. The
procedure involves comparing the fourier expansion of the IUPAC
convention of dihedral potential (equation 4.65) with the
Ryckaert-Bellemans (RB) functional of dihedral potential
(equation 4.62)
to get the Cn's of the RB function. However, I am not able to
understand
how to account for the phase angles. (Also to note, the parmbsc0
forcefield contains phase angles other than 0 and 180.)


Elegant conversion formulae require those angles to be convenient...

Mark


  Any advice or suggestion will be of great help.

Thank you,

Vignesh

--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the
world and a
desire to enjoy the world. This makes it hard to plan the day.
(E.B. White)

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--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)


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Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[gportel]

Hi,

Right, the only dihedral angles that do not allow an exact translation to
RB because of the phase are the ones involving the new parametrization for
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
populations of states right, thus avoiding the loss of helicity on the
long run. For proteins, there's no difference at all, so you can use
ffamber.

I've used the combined approach you mention without problems. The only
thing is that I do not use pdb2gmx. Rather I use amber's tools
(leap+libraries, all free in ambertools) to get a topology, and then I use
a slightly modified version of amb2gmx.pl script to get a gromacs
topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase
does not allow a direct conversion to RB form. Typically you have three
entries for the same dihedral, this is no problem at the itp level, grompp
captures them all. With this approach I reproduced a torsional scan of
parmbsc0 from amber md tool using gromacs, so I feel confident about it.

Another option is to use the ffamber parameters and change the itp file
including the new ones.

I should also mention that I had problems importing the new dihedrals
using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if
type 1 or 3 is used. There was a new dihedral type that could be used in
the development versions, but... for a reason it did not work out for me,
don't recall exactly why. It could well be that it would have worked with
more patience from my side.

Hope this helped, somehow. You were on the right direction anyway.

best,

Guillem


Mark Abraham wrote:
> On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:
>> Dear Dr. Mark,
>>
>> Thanks very much for pointing out that GROMACS can handle multiple
>> instances of the parameters with different n for a single dihedral.
>
> I hope I'm right there. There's been discussion on such topics before.
There's some subtle difference between [ dihedrals ] and [ dihedraltypes
] which eludes my memory, but which will be in the archives.
>
>> However, given that, in the existing ffamber ports in GROMACS  the other
>> dihedral parameters have been converted to RB form, would it make a
>> difference to just import these new parameters in the non-RB form?
>
> It will make no numerical difference, but g_energy will probably report
the contribution from the two different functional forms separately.
Attempting to mix *non-bonded* interactions in this kind of way asks for
trouble, because the maths is not well-defined. Here, you're fine,
because the maths is right.
>
>> To my knowledge, the torsional term should not vary (or, vary within
>> acceptable limits) irrespective of the functional form used to calculate
>> it. But I would like to know if there could be some reason for which
>> this assumption cannot be made.
>
> The R-B form might be more efficient to evaluate than a sum of simple
dihedrals in the cases where the angle is zero or 180, which might
explain the ffamber practice.
>
> Mark
>
>> Dear Dr. Alan,
>>
>> Thanks very much for pointing out to the acpypi code. I was able to
>> better understand the conversion procedure.
>>
>> Sincerely,
>> Vignesh
>>
>> On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham > > wrote:
>>
>> On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>>
>> Dear Users,
>>
>> I am trying to port the new parmbsc0 forcefield
>> (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs
for DNA
>> simulations.
>>
>> While unit conversions are sufficient to convert many of the
>> parameters
>> from AMBER to GROMACS format, dihedral angle conversion does not
>> seem to
>> be straight forward - the dihedral parameters need to be
>> converted to
>> the Ryckaert-Bellemans parameters.
>>
>>
>> Why? GROMACS can probably do the non-RB form - IIRC you can
>> implement a sum of multiple instances of 4.61 with different n.
>>
>>
>> I went through the GROMACS 4.0
>> manual, especially equations 4.61-4.65 to understand the
>> procedure. The
>> procedure involves comparing the fourier expansion of the IUPAC
>> convention of dihedral potential (equation 4.65) with the
>> Ryckaert-Bellemans (RB) functional of dihedral potential
>> (equation 4.62)
>> to get the Cn's of the RB function. However, I am not able to
>> understand
>> how to account for the phase angles. (Also to note, the parmbsc0
>> forcefield contains phase angles other than 0 and 180.)
>>
>>
>> Elegant conversion formulae require those angles to be convenient...
>>
>> Mark
>>
>>
>>   Any advice or suggestion will be of great help.
>>
>> Thank you,
>>



Dr. Guillem Portella
- MMB - Institute for Research in Biomedicine
- Parc Cientific de Barcelona -
http://mmb.pcb.ub.es/~gportella



-- 
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Re: [gmx-users] problem with total energy

[Justin A. Lemkul]

jampani srinivas wrote:

Hi
 
Thanks for your response, I am allowing the two groups (frozen and 
non-frozen) groups interact each other, i guess i am getting the energy 
of total system from g_energy.
 
I checked the velocities of frozen group atoms, they are not "zero". I 
have seen in git master that this problem was fixed and updated in md.c 
file, I have downloaded this from git master and compiled my gromacs 
again still i found that frozen atoms gets the initial velocity.
 
I am not at all clear why the energy of system should blow up, can you 
please help me if there is solution for this.
 


I haven't been following this closely; can you post an .mdp file?

-Justin


Thanks in advance.
 
Srinivas.


On Wed, Apr 7, 2010 at 4:47 PM, ms > wrote:


jampani srinivas ha scritto:
 > Dear Berk,
 >
 > I am sorry if i am confusing you with my poor description of problem,
 > actually I have submitted simulation with two temperature
coupling groups (i
 > think you already know that from our earlier conversations) and
found that
 > there is a continuous increase in the total energy of the system.
I could
 > not observe any blowing in the output file but the system energy is
 > continuously increasing, i am using 4fs time step here. Can you
please let
 > me know if i have to give more details?
 >

Which part of the system is increasing its energy?

m.
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--
*
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off: 215-895-1989
   Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Re: [gmx-users] problem with total energy

[jampani srinivas]

Dear Justin,

Thanks for your responce. Here is my mdp file.

+++
title   = AB2130
cpp = /usr/bin/cpp
constraints = all-bonds
integrator  = md
dt  = 0.004 ; ps !
nsteps  = 2500 ; total 100.0 ns.
nstcomm = 1
nstxout = 1000 ; collect data every 2.0 ps
nstvout = 1000 ; collect velocity every 2.0 ps
nstfout = 0
nstlog  = 0
nstenergy   = 1000 ; collect energy   every 2.0 ps
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.0
rvdw_switch = 0.9
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
tau_t   = 0.1  0.1
tc-grps = Tmp1 Tmp2
ref_t   = 283.00.0
gen_vel = yes
gen_temp= 283.0
acc_grps= Tmp1
accelerate  = 0.1 0.1 0.1
gen_seed= 181726
freezegrps  = Tmp2
freezedim   = Y Y Y

Thanks
Srinivas.
On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul  wrote:

>
>
> jampani srinivas wrote:
>
>> Hi
>>  Thanks for your response, I am allowing the two groups (frozen and
>> non-frozen) groups interact each other, i guess i am getting the energy of
>> total system from g_energy.
>>  I checked the velocities of frozen group atoms, they are not "zero". I
>> have seen in git master that this problem was fixed and updated in md.c
>> file, I have downloaded this from git master and compiled my gromacs again
>> still i found that frozen atoms gets the initial velocity.
>>  I am not at all clear why the energy of system should blow up, can you
>> please help me if there is solution for this.
>>
>>
>
> I haven't been following this closely; can you post an .mdp file?
>
> -Justin
>
> Thanks in advance.
>>  Srinivas.
>>
>>
>> On Wed, Apr 7, 2010 at 4:47 PM, ms > deviceran...@gmail.com>> wrote:
>>
>>jampani srinivas ha scritto:
>> > Dear Berk,
>> >
>> > I am sorry if i am confusing you with my poor description of
>> problem,
>> > actually I have submitted simulation with two temperature
>>coupling groups (i
>> > think you already know that from our earlier conversations) and
>>found that
>> > there is a continuous increase in the total energy of the system.
>>I could
>> > not observe any blowing in the output file but the system energy is
>> > continuously increasing, i am using 4fs time step here. Can you
>>please let
>> > me know if i have to give more details?
>> >
>>
>>Which part of the system is increasing its energy?
>>
>>m.
>>--
>>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
>>
>>
>>
>>
>> --
>> *
>> J. Srinivasa Rao
>> Post-doctoral Research Associate
>> C/o Prof. Luis R Cruz Cruz
>> Computational Biophysics Group
>> Department of Physics
>> Drexel University
>> 3141 Chestnut St
>> Philadelphia, PA 19104, USA.
>> Ph:  Off: 215-895-1989
>>   Mob:  704-706-4191
>> Web:http://jsrao.web.officelive.com/default.aspx
>> **
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 listgmx-users@gromacs.org
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>



-- 
*
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off: 215-895-1989
   Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**
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Re: [gmx-users] problem with total energy

[Justin A. Lemkul]

jampani srinivas wrote:

Dear Justin,
 
Thanks for your responce. Here is my mdp file.
 
+++

title   = AB2130
cpp = /usr/bin/cpp
constraints = all-bonds
integrator  = md
dt  = 0.004 ; ps !
nsteps  = 2500 ; total 100.0 ns.
nstcomm = 1
nstxout = 1000 ; collect data every 2.0 ps
nstvout = 1000 ; collect velocity every 2.0 ps
nstfout = 0
nstlog  = 0
nstenergy   = 1000 ; collect energy   every 2.0 ps
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.0
rvdw_switch = 0.9
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
tau_t   = 0.1  0.1
tc-grps = Tmp1 Tmp2
ref_t   = 283.00.0
gen_vel = yes
gen_temp= 283.0
acc_grps= Tmp1
accelerate  = 0.1 0.1 0.1
gen_seed= 181726
freezegrps  = Tmp2
freezedim   = Y Y Y



There are a whole host of reasons that you're seeing an energy drift.  Perhaps 
you should give a more detailed description of what you're trying to do.  Per 
your original message, you imply that you have a very simple system of some 
frozen and non-frozen group, which is clearly oversimplified.  A few thoughts:


1. You're applying constant acceleration, so you're introducing non-equilibrium 
conditions.  What is Tmp1?  Could it be working against Tmp2 (frozen) in some 
way that is causing a clash?


2. You're not using energrygrp_excl for your frozen group.  Per the manual:

"To avoid spurious contributions to the virial and pressure due to large forces 
between completely frozen atoms you need to use energy group exclusions, this 
also saves computing time."


3. Are you using virtual sites in addition to constraints?  Does a shorter 
timestep alleviate the energy drift?  Have a look at the Gromacs 4 paper for 
notes about use of virtual sites and constraints, and the effect on what's 
reasonable for the time step.


I'd suggest working through this systematically - you've got a ton of variables 
that could be opposing one another.  Introduce them one at a time to see where 
your system starts to break down.


-Justin


Thanks
Srinivas.
On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul > wrote:




jampani srinivas wrote:

Hi
 Thanks for your response, I am allowing the two groups (frozen
and non-frozen) groups interact each other, i guess i am getting
the energy of total system from g_energy.
 I checked the velocities of frozen group atoms, they are not
"zero". I have seen in git master that this problem was fixed
and updated in md.c file, I have downloaded this from git master
and compiled my gromacs again still i found that frozen atoms
gets the initial velocity.
 I am not at all clear why the energy of system should blow up,
can you please help me if there is solution for this.
 



I haven't been following this closely; can you post an .mdp file?

-Justin

Thanks in advance.
 Srinivas.


On Wed, Apr 7, 2010 at 4:47 PM, ms mailto:deviceran...@gmail.com> >> wrote:

   jampani srinivas ha scritto:
> Dear Berk,
>
> I am sorry if i am confusing you with my poor description
of problem,
> actually I have submitted simulation with two temperature
   coupling groups (i
> think you already know that from our earlier
conversations) and
   found that
> there is a continuous increase in the total energy of the
system.
   I could
> not observe any blowing in the output file but the system
energy is
> continuously increasing, i am using 4fs time step here.
Can you
   please let
> me know if i have to give more details?
>

   Which part of the system is increasing its energy?

   m.
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[gmx-users] gromos ffG653a6 parameters for MTSET

[Evelyne Deplazes]

Hi gmx-users

I am running a simulation on protein mutant that contains a cysteine with a
MTSET (methanethiosulfonate ethyltrimethyl ammonium OR
2-(trimethylammonium)ethyl methanethiosulfonate). since its not a standard
residue or solvent there are no parameters in the gromos force field. Yet
the molecule seems to be commonly used by experimentalists but I can only
find a single reference of simulation studies. Does anyone know of some
simulation studies or even has force field parameters for MTSET (or any of
the methanethiosulfonate reagents) ?

thanks

-- 
Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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Re: [gmx-users] problem with total energy

[jampani srinivas]

Dear Justin,


I am sorry for the poor description of the problem, OK let me explain you
clearly here.



I have taken a decapeptide and solvated it with box size 6.0 nm, I want to
create a frozen wall (confined sphere) around protein after a certain radius
(in this case it is 2.5 nm). To achieve this i made two temperature coupling
groups, first (Tmp1) one has protein and waters within 2.5nm from the center
of the box and rest is second temperature coupling group (Tmp2). Initially
when i run the simulation it was creating nrdf = 0 for both groups, Berk has
helped me with a file readir.c file, i compiled my gromacs again that
problem was solved. I have submitted simulations again and found that the
energy was blowing up. I think you know the story after this. Earlier I want
protein to interact with inner wall of the frozen group and check what
happens, because of this I have never looked at the energygrps_excl option.
I have done with both 2 and 4 fs time steps and I took 4fs option to speed
up the simulation, and I have to still look at the paper you suggested me.



Thanks for your suggestions, I have implemented your suggestion one after
the other, finally when i use the energygrps_excl option it worked out. Now
there is no sudden drift in the energy, and also i checked the velocities of
non-frozen group is mostly zero (except for first frame)



When I use the energygrps_excel option in the following way i am getting the
below mentioned note i have to still understand what is this message. On the
other hand if i use only "energygrp_excl  = Tmp2 Tmp2 Tmp2 Tmp1"  line in
mdp file i am getting fatal error. Is it necessary to to define the energy
groups first and later exclude the energy option?

+

energygrps = Tmp1 Tmp2
energygrp_excl  = Tmp2 Tmp2 Tmp2 Tmp1



NOTE

"Can not exclude the lattice Coulomb energy between energy groups"

I used -maxwarn option here and generated the tpr file. I hope this does not
harm the simulation.



Please let me know your comments and suggestion.



Thanks very much for your kind help.



Srinivas.


On Thu, Apr 8, 2010 at 8:21 PM, Justin A. Lemkul  wrote:

>
>
> jampani srinivas wrote:
>
>> Dear Justin,
>>  Thanks for your responce. Here is my mdp file.
>>  +++
>> title   = AB2130
>> cpp = /usr/bin/cpp
>> constraints = all-bonds
>> integrator  = md
>> dt  = 0.004 ; ps !
>> nsteps  = 2500 ; total 100.0 ns.
>> nstcomm = 1
>> nstxout = 1000 ; collect data every 2.0 ps
>> nstvout = 1000 ; collect velocity every 2.0 ps
>> nstfout = 0
>> nstlog  = 0
>> nstenergy   = 1000 ; collect energy   every 2.0 ps
>> nstlist = 10
>> ns_type = grid
>> rlist   = 1.0
>> coulombtype = PME
>> rcoulomb= 1.0
>> rvdw= 1.0
>> rvdw_switch = 0.9
>> 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
>> tau_t   = 0.1  0.1
>> tc-grps = Tmp1 Tmp2
>> ref_t   = 283.00.0
>> gen_vel = yes
>> gen_temp= 283.0
>> acc_grps= Tmp1
>> accelerate  = 0.1 0.1 0.1
>> gen_seed= 181726
>> freezegrps  = Tmp2
>> freezedim   = Y Y Y
>> 
>>
>
> There are a whole host of reasons that you're seeing an energy drift.
>  Perhaps you should give a more detailed description of what you're trying
> to do.  Per your original message, you imply that you have a very simple
> system of some frozen and non-frozen group, which is clearly oversimplified.
>  A few thoughts:
>
> 1. You're applying constant acceleration, so you're introducing
> non-equilibrium conditions.  What is Tmp1?  Could it be working against Tmp2
> (frozen) in some way that is causing a clash?
>
> 2. You're not using energrygrp_excl for your frozen group.  Per the manual:
>
> "To avoid spurious contributions to the virial and pressure due to large
> forces between completely frozen atoms you need to use energy group
> exclusions, this also saves computing time."
>
> 3. Are you using virtual sites in addition to constraints?  Does a shorter
> timestep alleviate the energy drift?  Have a look at the Gromacs 4 paper for
> notes about use of virtual sites and constraints, and the effect on what's
> reasonable for the time step.
>
> I'd suggest working through this systematically - you've got a ton of
> variables that could be opposing one another.  Introduce them one at a time
> to see where your system starts to break down.
>
> -Justin
>
> Thanks
>> Srinivas.
>>
>> On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>jampani srinivas wrote:
>>
>>Hi
>>   

Re: [gmx-users] Simulation of only Lipid Bilayer

[Arun kumar V]

On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul  wrote:

>
>
> Arun kumar V wrote:
>
>> Try PRODRG server to build the molecule as well as to get topology file.
>> Though  you might have to be careful in using this topology file.
>>
>>
> If by "be careful" you mean "don't use this topology," I'll agree :)  The
> Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1, given by
> PRODRG) fall far short of reproducing lipid properties.  That, and the
> charges assigned by PRODRG for lipids will not resemble any known parameter
> set, requiring a complete re-write of this topology.  You could use PRODRG
> to build the molecule, but there are a number of other programs that can do
> that as well (see the Gromacs site for a list).
>
> To the original post: What lipid are you looking to simulate?  Many
> pre-equilibrated lipid bilayers are available in the public domain, along
> with suitable paramters, saving you a lot of work in building these systems.
>  They can be tricky.
>
> -Justin
>
>
> @Justin
 I agree with you. Currently I am not actively involving with
gromacs simulations but planning to involve. I have not been to GROMACS
website from long time. In fact the version I have used last time is gromacs
3.3(almost 2 years back). There is lot of progress ofcourse.

Thanks,
Arun

 Arun
>>
>> Saumya wrote:
>>
>>> Hi all,
>>>
>>> Well, I have been trying to make lipid bilayers using genconf of
>>> gromacs from a single lipid molecule.
>>> Can anyone tell me how to proceed with the simulation of lipid
>>> bilayers starting with a single lipid molecule?
>>> How can I obtain the .pdb file for a lipid?
>>> Is there any manual that describes the procedure using Gromacs?
>>>
>>> Hoping for some inputs.
>>>
>>> Regards
>>> Saumya
>>>
>>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



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Re: [gmx-users] InflateGRO and pentamer protein simulation

[xi zhao]

I would like to run a simulation of a pentamers in a POPC membrane,  and using 
new inflategro with doughnut mode, but I have met similar  result as the links  
http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also  
got a lot of errors about uninitialized values. When the script finishes, the 
membrane is rescaled, but the protein is untouched in the corner of the new 
box. Please give me some suggestions! Thank you in  advance!
> best regards!





--- 10年4月9日，周五, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] InflateGRO and pentamer protein simulation
收件人: "Discussion list for GROMACS users" 
日期: 2010年4月9日,周五,上午2:14




xi zhao wrote:
> 
> 
> Dear sir :
> I want to a pentamer membrane protein, when I used InflateGRO.pl with 
> /DOUGHNUT Mode, the results were wrong, please help me! /

If you want any useful help, you'll have to do a whole lot better than simply 
saying "the results were wrong."  No one on this list will have any idea what 
you mean.  If you believe there is some error in the script itself, you're 
better off contacting its author.

-Justin

> 4 
> show
>  " [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 
> kk_inflated.gro 5 area.dat doughnut protein_subunits
> Doughnut mode activated. Protein coordinates will be translated by subunit 
> 
> Reading.
> Reading chain identifiers
> Subunit 1:  atom 1 to  atom 3238
> Subunit 2:  atom 3239 to  atom 6476
> Subunit 3:  atom 6477 to  atom 9714
> Subunit 4:  atom 9715 to  atom 12952
> Subunit 5:  atom 12953 to  atom 16190
> There are 5 protein subunits
> Scaling lipids
> There are 512 lipids...
> with 65 atoms per lipid..
> Determining upper and lower leaflet...
> 256 lipids in the upper...
> 256 lipids in the lower leaflet
> Checking for overlap
> ...this might actually take a while...
> ...
> Argument "N4" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C5" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C6" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "O7" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "P8" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "O9" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "A1" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "A2" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C1" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C2" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C3" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "N4" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C5" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "C6" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "O7" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "P8" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "O9" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "A1" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Argument "A2" isn't numeric in printf at inflategro.txt line 708,  
> line 5.
> Calculating Area per lipid...
> Protein X-min/max: 23    105
> Protein Y-min/max: 18    100
> X-range: 82 A    Y-range: 82 A
> Building 82 X 82 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD
> lower TMD
> Area per protein: 49 nm^2
> Area per lipid: 9.83158146861789 nm^2
> Area per protein, upper half: 38.75 nm^2
> Area per lipid, upper leaflet : 9.79362516645161 nm^2
> Area per protein, lower half: 45.75 nm^2
> Area per lipid, lower leaflet : 9.92548787409836 nm^2
> Writing Area per lipid...
> Done!
> 
> 
>  

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Re: [gmx-users] problem with total energy

[Mark Abraham]

On 9/04/2010 1:25 PM, jampani srinivas wrote:

Dear Justin,

I am sorry for the poor description of the problem, OK let me explain
you clearly here.

I have taken a decapeptide and solvated it with box size 6.0 nm, I want
to create a frozen wall (confined sphere) around protein after a certain
radius (in this case it is 2.5 nm). To achieve this i made two
temperature coupling groups, first (Tmp1) one has protein and waters
within 2.5nm from the center of the box and rest is second temperature
coupling group (Tmp2). Initially when i run the simulation it was
creating nrdf = 0 for both groups, Berk has helped me with a file
readir.c file, i compiled my gromacs again that problem was solved. I
have submitted simulations again and found that the energy was blowing
up. I think you know the story after this. Earlier I want protein to
interact with inner wall of the frozen group and check what happens,
because of this I have never looked at the energygrps_excl option. I
have done with both 2 and 4 fs time steps and I took 4fs option to speed
up the simulation, and I have to still look at the paper you suggested me.

Thanks for your suggestions, I have implemented your suggestion one
after the other, finally when i use the energygrps_excl option it worked
out. Now there is no sudden drift in the energy, and also i checked the
velocities of non-frozen group is mostly zero (except for first frame)

When I use the energygrps_excel option in the following way i am getting
the below mentioned note i have to still understand what is this
message. On the other hand if i use only "energygrp_excl  = Tmp2 Tmp2
Tmp2 Tmp1"  line in mdp file i am getting fatal error. Is it necessary
to to define the energy groups first and later exclude the energy option?


Yes, energy group exclusions require matching energy group definitions. 
The relevant part of manual 7.3 probably says this.



+

energygrps = Tmp1 Tmp2
energygrp_excl  = Tmp2 Tmp2 Tmp2 Tmp1



NOTE

"Can not exclude the lattice Coulomb energy between energy groups"


You seem to be trying to simulate a droplet inside a rigid shell of 
water. If so, why do you want the system to be periodic? You don't want 
periodicity artefacts *and* frozen-water-shell artefacts. There are 
other electrostatics models better suited than PME to such situations. 
You should look in the literature for successful published 
methodologies, rather than risk inventing a square wheel yourself before 
you've got enough experience to be confident with what you're doing.


Here, the reciprocal-space part of the PME calculation must contain 
contributions from your excluded energy-groups, so you've got some 
Frankenstein possible worst-of-all-worlds combination. If I got such a 
paper to review, I'd need to see some serious groundwork justifying such 
a choice.



I used -maxwarn option here and generated the tpr file. I hope this does
not harm the simulation.


That's a risky strategy. The programmer didn't put in such a message 
just to see whether he could do it...


Mark
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Re: [gmx-users] gromos ffG653a6 parameters for MTSET

[Mark Abraham]

On 9/04/2010 1:21 PM, Evelyne Deplazes wrote:

Hi gmx-users

I am running a simulation on protein mutant that contains a cysteine
with a MTSET (methanethiosulfonate ethyltrimethyl ammonium OR
2-(trimethylammonium)ethyl methanethiosulfonate). since its not a
standard residue or solvent there are no parameters in the gromos force
field. Yet the molecule seems to be commonly used by experimentalists
but I can only find a single reference of simulation studies. Does
anyone know of some simulation studies or even has force field
parameters for MTSET (or any of the methanethiosulfonate reagents) ?


I don't know of any. It'd be rare enough for any force field to have 
sulfate parameters, never mind thiosulfonate. Consider the points 
mentioned here 
http://www.gromacs.org/Documentation/How-tos/Parameterization.


Mark
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[gmx-users] Joining two peptide chains

[Anirban Ghosh]

Hi ALL,

Is there any way in GROMACS to join two peptide chains by forming a peptide
bond between the C and N atoms?
Any suggestion is welcome.

Regards,

Anirban
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[gmx-users] g_sas => micelle ?

[Chih-Ying Lin]

HI
how to calculate SASA of micelle using g_sas?
i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the
atom numbers of micelle.


if micelle is not compact enough but there are no water molecules inside the
micelle, will g_sas calculate the vacancy part inside the micelle?

Or, if there exists water molecules inside the micelle, will g_sas calculate
the water/micelle interface part inside the micelle?


Thank you
Lin
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[gmx-users] Random Accelerator Molecular Dynamics

[babu gokul]

Hi all
I would like to know whether  Random Accelerator Molecular Dynamics is 
available in Gromacs as it is available in AMBER. 

E R Azhagiya singam

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