RE: [gmx-users] using xmp file

[pragya chohan]

Hi 
i found out the residues which form H bond but am still not able to get life 
time if H bond. The option -lifetime gives t as x and p(t) as y axis. is this 
value for all the bonds. 
How can i see the lifetime of each bond?
 
Thanking you
 
pragya chohan
> Date: Sat, 3 May 2008 02:06:52 +0200> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: Re: [gmx-users] using xmp file> > Mark 
> Abraham wrote:> > pragya chohan wrote:> >> Dear users> >> > >> I wasted to 
> look at H bonding between between a particular residue> >> and rest of the 
> system. So I did g_hbond. It created a number of> >> files I want to make a 
> table indicating atom of residue> >> participating, atom or residue number of 
> Donor atom, lifetime of> >> those bonds to show their significance.> >> > >> 
> Can you tell me which files are useful for this purpose? > >> > Yes, but 
> first you should be reading "g_hbond -h" and working some> > things out for 
> yourself.> >> >> Also please tell me how to visualise xmp files on windows>> 
> >> > Google is probably your friend for finding out about viewers for *xpm*> 
> > files. The GIMP will certainly work, but it's a heavyweight solution!> >> 
> Perhaps the xpm2ps tool will also help to view a ps document, which> should 
> be possible with windows ;)> > > > Mark> > 
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[gmx-users] using xmp file

[pragya chohan]

Dear users
 
I wasted to look at H bonding between between a particular residue and rest of 
the system. So I did g_hbond. It created a number of files I want to make a 
table indicating atom of residue participating, atom or residue number of Donor 
atom, lifetime of those bonds to show their significance.
 
Can you tell me which files are useful for this purpose? Also please tell me 
how to visualise xmp files on windows>
 
Thanking You
 
Pragya Chohan
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[gmx-users] problem with g_order

[pragya chohan]

Dear users
 
I am calculating order parameters of palmitoyl which has 16 carbons. I made the 
index file with all 16 atoms selected . but the output file has only 14 atoms 
listed.
 
I have cross-checked the index file. what can be the problem?
 
I am using 3.3 version
 
Thanking you
 
Pragya Chohan
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[gmx-users] area compressibility modulus

[pragya chohan]

Hi read a paper quoted in the previous post. It calculated area compressibility 
by : Area compressibility moduli were approximated by using surface tension and 
APL differencesobtained in simulations. 
 
Can anyone please explain what the procedure really is?
 
Thanking You
 
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[gmx-users] request

[pragya chohan]

Dear user
 
Can anyone please send me the below mentioned journal paper
"Performance of the general amber force field in modeling aqueous POPC membrane 
bilayers" thw link is 
http://www3.interscience.wiley.com/journal/114209721/abstract. Mu institute 
does not have access.
 
I will be very thankful. My address id [EMAIL PROTECTED]
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[gmx-users] help regarding analysis

[pragya chohan]

Dear users
 
I have run a protein XX in water. According to literature, it is supposed to 
undergo tertiary structure changes without much secondary structure changes.
 
Can anyone help me with what can be a suitable analysis method for it.
The other changes reported include 1. change in hydrophobicity - which I have 
done 
2. some change from helix to coil which I have done through do_dssp
 
Any other suggestion is appreciated
 
Thanking You
 
Pragya Chohan
 
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RE: [gmx-users] area per lipid

[pragya chohan]

Hi 
 
I have read the reference quoted there and they have given the time evolution 
of area per head-group to decrease and become constant near that value 
(including last snapshot). 
 
Is the way described in earlier post correct? According to what I have seen, 
the structure at peter tieleman's site also has dimensions around 62-63 
angstoms and average area per lipid is qouted by them is also around the same.
 
the value of box-x and box-y i got from g_energy is also fluctuating b/w 
6.2-6.3 nm. I want to see time evolution of area per lipid?
 
I want to show that the bilayer model satisfies all the experimental results 
before going further.
 
Any suggestion is welcome.
> Date: Mon, 28 Apr 2008 22:25:56 -0400> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: Re: [gmx-users] area per lipid> > Quoting 
> pragya chohan <[EMAIL PROTECTED]>:> > >> > dear users> >> > I am trying to 
> calculate area per lipid. I have downloaded the structure from> > 
> http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.> >> > Earlier posts say 
> that area per lipid can be calculated as box-x*box-y> > /#no.of lipids per 
> monolayer. what I fail to understand is> > 64.841*63.993/64 is not equal to 
> 0.658 +/- 0.009.> >> > the box-x and box-y are calculated from g_energy. Am I 
> understanding> > something wrong?> > The reference for this particular lipid 
> says that the _average_ area per> headgroup is 0.658 +/- 0.009, not that the 
> ending structure of the simulation> will have exactly that area per lipid. 
> There is definitely going to be some> fluctuation along the trajectory, and 
> the last frame is just a snapshot.> > -Justin> > >> > Please help> >> > 
> Pragya Chohan> > 
> _> > Fashion 
> Channel : Want to know what’s the latest in the fashion world ? You> > have 
> it all here on MSN Fashion.> > http://lifestyle.in.msn.com/> > > > 
> > > Justin A. Lemkul> Graduate 
> Research Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, 
> VA> [EMAIL PROTECTED] | (540) 231-9080> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> > 
> ___> gmx-users mailing list 
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[gmx-users] area per lipid

[pragya chohan]

dear users
 
I am trying to calculate area per lipid. I have downloaded the structure from 
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml. 
 
Earlier posts say that area per lipid can be calculated as box-x*box-y /#no.of 
lipids per monolayer. what I fail to understand is 
64.841*63.993/64 is not equal to 0.658 +/- 0.009. 
 
the box-x and box-y are calculated from g_energy. Am I understanding something 
wrong?
 
Please help
 
Pragya Chohan
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[gmx-users] anisotropic coupling tau_p values

[pragya chohan]

hi 
please refer to my mail 
http://www.gromacs.org/pipermail/gmx-users/2008-March/033024.html I posted a 
question regarding taup_p to be used with anisotropic coupling. 
As qoted "A reasonable choice for relaxation time would be 100 fs. The 
compressibility and the relaxation time appear only as a ratio in the dynamics, 
so a larger compressibility is equivalent to a smaller relaxation time."
I want to ask if we can give the value of tau_p 0.0 for diagonal elements while 
specifying for anisotropic coupling. 
Both tau_p 0.0 as well as 1.0 continue to run. 

Any comments would be appreciated

Cheers
Pragya Chohan
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RE: [gmx-users] Question about different versions of gromacs

[pragya chohan]

hi .. 


From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: RE: [gmx-users] Question about 
different versions of gromacsDate: Fri, 28 Mar 2008 12:40:34 +0100



Hi,In minor releases (3.3.?) the tpr file format does not change.Also 
simulation results should not change, unless a bug was fixed which affects your 
simulations.
 
I want to continue a simulation in gromacs 3.3.1 which was earlier ran in 
gromacs 3.3. Can i also do that  as you say that results are not affected? 
Berk.

> Date: Fri, 28 Mar 2008 11:25:06 +0100> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: Re: [gmx-users] Question about different 
> versions of gromacs> > Hi Nicolas,> > it is no problem to read 'older' tpr 
> files with a newer version of > gromacs. The other way round, it will 
> probably not work - but gromacs > will give you an error message then, 
> displaying the version differences.> > Carsten> > > Nicolas Martinez wrote:> 
> > Hello gromacs users> > I am using gromacs to perform MD simulations of a 
> protein in a box of > > water.> > My run input files (tpr file)are being 
> prepared on my local machine > > which has gromacs version 3.3.1 but my 
> calculations are made on a > > different machine who has gromacs 3.3.2.> > 
> Should I be doing this?> > Thanks in advance> > Nicolas Martinez> > 
> ___> > gmx-users mailing list 
> gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users> > 
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[gmx-users] lipid parameters for ffG43a1

[pragya chohan]

Hello users
Is there anyone running simulation of lipid bilayers in ffG43a1 or any other 
force field apart from ffgmx?
Could anyone tell me how to compile a patch into already installed Gromacs . I 
have 3.3 in my system and want to comile a patch for secondary structure 
prediction.

Cheers
Pragya Chohan

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[gmx-users] information about tau_p

[pragya chohan]

 Hi users
 
Can you please tell me if in an anisotropic pressure coupling type the diagonal 
pau_p should be 0 or not. And how it can affect our simulation. What I mean is:
I have ref_p = 1.0 1.0 1.0 0 0 0
With that is it better to use tau_p= 1.0 1.0 1.0 0 0 0
or tau_p =1 1 1 1 1 1 
and please tell me what kind of difference it can cause? As according to the 
formula tau_p comes in denominator and value 0 should not be used. Please tell 
me if I am wrong.
 
Cheers
 
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RE: [gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

Thanks for your reply. Can you tell me which one is a better way for carrying 
out the simulation?


> Date: Mon, 17 Mar 2008 09:13:03 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] understanding of difference between gromacs 
> procedures
> 
> Quoting pragya chohan <[EMAIL PROTECTED]>:
> 
> >
> > the step is indeed equillibration ... thanks for the reply  so can we 
> > say
> > that the second step will produce entirely different results throughout or
> > will it be a matter of only time of simulation needed?
> 
> Well, it's hard to say definitively, but if you want to replicate results and
> are preparing your systems differently, I wouldn't count on getting anything
> that correlates.
> 
> -Justin
> 
> > Date: Mon, 17 Mar
> > 2008 08:30:49 -0400> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org>
> > Subject: RE: [gmx-users] understanding of difference between gromacs
> > procedures> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > One
> > of my lab-mates> > > > is doing the same system by following a different
> > procedure (difference> > > > listed below)> > > > I did position restrain by
> > define = -DPOSRES -DPOSRES_LIPID> > > > and he is doing define = -DPOSRES> >
> > > > and then for lipid.> > >> > > I don't understand what you mean by this.>
> > > one of us are putting restrain on both protein and lipid and removing> >
> > restrain from first lipid while keeping force on the protein and then> >
> > removing restrain from protein whereas other one is only putting restrain 
> > on>
> > > protein first and after removing the restrain from protein then applies> >
> > restrain to the lipid .> > So one approach is to progressively remove
> > restraints, while the other seems to> remove restraints and add them back on
> > in different groups. I would think the> more correct approach would be the
> > first, but you still haven't told us what> step this is. Minimization?
> > Equilibration?> > It seems to me that if this is an equilibration, you are
> > certain to see> differences, as Mark has already pointed out. If this is a
> > minimization, the> second procedure of removing and re-adding restraints
> > seems to make no sense to> me.> > -Justin> > > > > Rest of the procedure is
> > the same.> > > > He got conformational change within 250 ps and I did not 
> > get
> > till 2ns> > > > even though we use same parameters on mdp and have same
> > starting> > structure.> > > >> > > > Can anyone give some insight what may 
> > be
> > the logic for this difference?> > >> > > If one of you is
> > position-restraining your lipids and one isn't, surely> > > the fact that 
> > you
> > get conformational change at a different time is> > expected.> > >> > >
> > You've also not said whether anybody is removing position restraints at> > >
> > any stage of the MD.> > >> > > Mark> > >
> > ___> > > gmx-users mailing list
> > gmx-users@gromacs.org> > > 
> > http://www.gromacs.org/mailman/listinfo/gmx-users>
> > > > Please search the archive at http://www.gromacs.org/search before
> > posting!> > > Please don't post (un)subscribe requests to the list. Use the>
> > > > www interface or send it to [EMAIL PROTECTED]> > > Can't
> > post? Read http://www.gromacs.org/mailing_lists/users.php> >> >
> > _> > Post
> > free property ads on Yello Classifieds now! www.yello.in> >>
> >
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> > > gmx-users mailing list gmx-users@gromacs.org> >
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> > > > Justin A. Lemkul> Graduate
&g

RE: [gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

the step is indeed equillibration ... thanks for the reply  so can we say 
that the second step will produce entirely different results throughout or will 
it be a matter of only time of simulation needed?> Date: Mon, 17 Mar 2008 
08:30:49 -0400> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: 
RE: [gmx-users] understanding of difference between gromacs procedures> > 
Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > One of my lab-mates> > > > 
is doing the same system by following a different procedure (difference> > > > 
listed below)> > > > I did position restrain by define = -DPOSRES 
-DPOSRES_LIPID> > > > and he is doing define = -DPOSRES> > > > and then for 
lipid.> > >> > > I don't understand what you mean by this.> > one of us are 
putting restrain on both protein and lipid and removing> > restrain from first 
lipid while keeping force on the protein and then> > removing restrain from 
protein whereas other one is only putting restrain on> > protein first and 
after removing the restrain from protein then applies> > restrain to the lipid 
.> > So one approach is to progressively remove restraints, while the other 
seems to> remove restraints and add them back on in different groups. I would 
think the> more correct approach would be the first, but you still haven't told 
us what> step this is. Minimization? Equilibration?> > It seems to me that if 
this is an equilibration, you are certain to see> differences, as Mark has 
already pointed out. If this is a minimization, the> second procedure of 
removing and re-adding restraints seems to make no sense to> me.> > -Justin> > 
> > > Rest of the procedure is the same.> > > > He got conformational change 
within 250 ps and I did not get till 2ns> > > > even though we use same 
parameters on mdp and have same starting> > structure.> > > >> > > > Can anyone 
give some insight what may be the logic for this difference?> > >> > > If one 
of you is position-restraining your lipids and one isn't, surely> > > the fact 
that you get conformational change at a different time is> > expected.> > >> > 
> You've also not said whether anybody is removing position restraints at> > > 
any stage of the MD.> > >> > > Mark> > > 
___> > > gmx-users mailing list 
gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users> > 
> Please search the archive at http://www.gromacs.org/search before posting!> > 
> Please don't post (un)subscribe requests to the list. Use the> > > www 
interface or send it to [EMAIL PROTECTED]> > > Can't post? Read 
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 > gmx-users mailing list gmx-users@gromacs.org> > 
http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive 
at http://www.gromacs.org/search before posting!> > Please don't post 
(un)subscribe requests to the list. Use the> > www interface or send it to 
[EMAIL PROTECTED]> > Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php> >> > > > 
> > Justin A. Lemkul> Graduate Research 
Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL 
PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> 
___> gmx-users mailing list 
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RE: [gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

One of my lab-mates 
> > is doing the same system by following a different procedure (difference 
> > listed below)
> > I did position restrain by define = -DPOSRES -DPOSRES_LIPID
> >  and he is doing define = -DPOSRES
> >  and then for lipid.
> 
> I don't understand what you mean by this.
one of us are putting restrain on both protein and lipid and removing restrain 
from first lipid while keeping force on the protein and then removing restrain 
from protein whereas other one is only putting restrain on protein first and 
after removing the restrain from protein then applies restrain to the lipid .
> > Rest of the procedure is the same.
> > He got conformational change within 250 ps and I did not get till 2ns
> > even though we use same parameters on mdp and have same starting structure.
> >  
> > Can anyone give some insight what may be the logic for this difference?
> 
> If one of you is position-restraining your lipids and one isn't, surely 
> the fact that you get conformational change at a different time is expected.
> 
> You've also not said whether anybody is removing position restraints at 
> any stage of the MD.
> 
> Mark
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[gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

hello gmx users
I am doing a simulation of protein in membrane after simulating a protein in 
water and inserting it into a membrane. One of my lab-mates is doing the same 
system by following a different procedure (difference listed below)
I did position restrain by define = -DPOSRES -DPOSRES_LIPID
 and he is doing define = -DPOSRES
 and then for lipid. 
Rest of the procedure is the same. 
He got conformational change within 250 ps and I did not get till 2ns 
even though we use same parameters on mdp and have same starting structure.
 
Can anyone give some insight what may be the logic for this difference?
 
I can send gro files off the list for anyone willing to help.
 
Thanking You
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RE: [gmx-users] calculating B-factor

[pragya chohan]

thanks for your reply.. but that command gives B-Factor by atom. Is it possible 
to get by residue... > From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> 
Subject: Re: [gmx-users] calculating B-factor> Date: Mon, 18 Feb 2008 12:46:43 
+0200> > Hi,> > check out g_rmsf (options -oq, -q, -ox), rmsf can be converted 
into B-factors.> > > Best regards,> > Björn> > > > > > Dear users> > Is it 
posible to calculate B-factor for a protein using gromacs?> > Pragya> >> > 
> > Detailed profiles 4 marriage! Only at 
Shaadi.com Try> > it!> > -- > Dr. 
Björn Windshügel> > Department of Pharmaceutical Chemistry> University of 
Kuopio> P.O. Box 1627> 70211 Kuopio, FINLAND> > Email: [EMAIL PROTECTED]> 
Phone: (+358) 17 162463> Fax: (+358) 17 162456> Web: 
www.uku.fi/farmasia/fake/modelling/index.shtml> 
___> gmx-users mailing list 
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[gmx-users] calculating B-factor

[pragya chohan]

Dear users
Is it posible to calculate B-factor for a protein using gromacs?
Pragya
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RE: [gmx-users] fatal error in g_order

[pragya chohan]

I had made groups using make_ndx command and selected say "a C12|a C13." 
and named one group as palmitoyl and other group as oleoyl but when I select 
these groups during the execution of commamd  get the error:
> > Groupname: System First atomname: C1 First atomnr 0> > Groupname: POPC 
> > First atomname: C1 First atomnr 0> > Groupname: SOL First atomname: OW 
> > First atomnr 6656> > Groupname: oleoyl First atomname: C1 First atomnr 
> > 1820> > Groupname: palmitoyl First atomname: C1 First atomnr 832> >> > 
> > Reading frame 0 time 0.000 Number of elements in first group:> > 14036> > 
> > ---> > Program g_order, 
> > VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> 
> > > grp 1 does not have same number of elements as grp 1
 
Is there something I am doing wrong? something I dont know of while using 
g_oder. I have read the mailing list and made groups accordingly.
One more question: In the mailing list it was wriiten to make separate group 
for CH3, CH2,CH. Is that the mistake I am doing since I am specifying the whole 
chain. > Date: Sun, 3 Feb 2008 12:38:43 -0500> From: [EMAIL PROTECTED]> To: 
gmx-users@gromacs.org> Subject: Re: [gmx-users] fatal error in g_order> > > 
This issue is well-documented in the list archives. You need to create an 
index> group that specifies *only* the groups of interest in the index file, 
i.e. C16,> C17...> > There is a post (I believe from Dallas Warren) that even 
gives examples of> make_ndx commands to create such groups, if you need that 
kind of help.> > -Justin> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > 
hi> > I am trying to do the bilayer analysis and want to calculate order 
parameters> > using g_order. I made the index using make_ndx command and 
selected the> > carbons sai 1-16 of my first chain and 17-33 of the other in 
same index file> > as two separate group. When I am giving this index file to 
g_order I get the> > error:> >> > Using following groups:> > Groupname: System 
First atomname: C1 First atomnr 0> > Groupname: POPC First atomname: C1 First 
atomnr 0> > Groupname: SOL First atomname: OW First atomnr 6656> > Groupname: 
oleoyl First atomname: C1 First atomnr 1820> > Groupname: palmitoyl First 
atomname: C1 First atomnr 832> >> > Reading frame 0 time 0.000 Number of 
elements in first group:> > 14036> > 
---> > Program g_order, 
VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> > 
grp 1 does not have same number of elements as grp 1> >> > Please help.> >> > 
_> > Tried the 
new MSN Messenger? It’s cool! Download now.> >> 
http://messenger.msn.com/Download/Default.aspx?mkt=en-in___>
 > gmx-users mailing list gmx-users@gromacs.org> > 
http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive 
at http://www.gromacs.org/search before posting!> > Please don't post 
(un)subscribe requests to the list. Use the> > www interface or send it to 
[EMAIL PROTECTED]> > Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php> >> > > > 
> > Justin A. Lemkul> Graduate Research 
Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL 
PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> 
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[gmx-users] fatal error in g_order

[pragya chohan]

hi
I am trying to do the bilayer analysis and want to calculate order parameters 
using g_order. I made the index using make_ndx command and selected the carbons 
sai 1-16 of my first chain and 17-33 of the other in same index file as two 
separate group. When I am giving this index file to g_order I get the error:

Using following groups:
Groupname: System First atomname: C1 First atomnr 0
Groupname: POPC First atomname: C1 First atomnr 0
Groupname: SOL First atomname: OW First atomnr 6656
Groupname: oleoyl First atomname: C1 First atomnr 1820
Groupname: palmitoyl First atomname: C1 First atomnr 832

Reading frame   0 time0.000   Number of elements in first group: 14036
---
Program g_order, VERSION 3.3
Source code file: gmx_order.c, line: 160

Fatal error:
grp 1 does not have same number of elements as grp 1

Please help.

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RE: [gmx-users] analysis of POPC

[pragya chohan]

Thanks, but I did get some papers on the analysis done on POPC by MD but I did 
not get any experimental papers showing the values so that I can compare 
results of my MD with experimental data.
If anyone happens to have such papers please send them to me at [EMAIL 
PROTECTED]> Date: Sat, 2 Feb 2008 07:20:54 -0500> From: [EMAIL PROTECTED]> To: 
gmx-users@gromacs.org> Subject: Re: [gmx-users] analysis of POPC> > Quoting 
pragya chohan <[EMAIL PROTECTED]>:> > >> > hello users> > I am trying to do 
analysis after bilayer simulation. I cannot get any> > experimental data on 
POPC to validate my model with. Can the people who are> > working on same lipid 
tell me some references and also what analysis should> > be done of the bilayer 
before putting protein into it?> > I spent less than two minutes on Google and 
found papers giving all sorts of> experimental parameters (density, area per 
headgroup, bilayer thickness, etc). > I suggest you try the same.> > In terms 
of the analysis you need to do, that is up to what question you are> asking and 
why you are simulating this particular lipid. Refer to the> literature and find 
papers by groups that have simulated proteins in POPC (and> perhaps proteins in 
membranes in general) to determine what they have found> relevant, and apply 
the same to your system.> > -Justin> > > 
_> > Tried the 
new MSN Messenger? It’s cool! Download now.> > 
http://messenger.msn.com/Download/Default.aspx?mkt=en-in> > > > 
> > Justin A. Lemkul> Graduate Research 
Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL 
PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> 
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[gmx-users] analysis of POPC

[pragya chohan]

hello users
I am trying to do analysis after bilayer simulation. I cannot get any 
experimental data on POPC to validate my model with. Can the people who are 
working on same lipid tell me some references and also what analysis should be 
done of the bilayer before putting protein into it?
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[gmx-users] concatenate tpr file

[pragya chohan]

hi users
I want todo analysis of my bilayer. So i order to process all trr files I 
concatenated them with trjcat . Is it also possible to concatenate tpr files in 
a similar way or I have to fo it imdividually for each trajectory?
pragya
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[gmx-users] information for analysis

[pragya chohan]

hello users
please can you tell me how to calculate surface area per lipid, orer 
parameters, area per head group of lipid from simulation
thanks in advance
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[gmx-users] membrane protein simulation

[pragya chohan]

hello users
I am starting a membrane protein simulation. I had some missing residues in the 
protein which have been added now. Should I minimise in vaccum before insertion 
of the protein in bilayer? 
Another question : Is it necessary to do simulation in water before inserting 
protein nto bilayer?
 
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RE: [gmx-users] problem in bilayer simulation

[pragya chohan]

> I understood that it is a periodic boundry condition problem and used
>  trjconv. But it writes a trajectory file. How do I make a gro file to
> input it into next run
Thanks I guess I was wrong. trjconv does write gro files. 
In any case, working out
> how to do the restart is totally separate from any post-processing you've
> done for visualization purposes.
Ya i want to post process my file and not restart it. I am using the command
trjconv -f md.gro -pbc inbox -center rect -o processed.gro
I have gromacs 3.3.1 version. Am I using the correct command. I want to put all 
the water displaced back so that my initial rectangular structure is conserved.

> Date: Tue, 1 Jan 2008 14:41:09 +1100
> Subject: RE: [gmx-users] problem in bilayer simulation
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> 
> >
> >
> > I think you misunderstood my reply.
> > I understood that it is a periodic boundry condition problem and used
> > trjconv. But it writes a trajectory file. How do I make a gro file to
> > input it into next run?
> 
> Depending on what you're doing, you may not need one. See
> http://wiki.gromacs.org/index.php/Doing_Restarts. In any case, working out
> how to do the restart is totally separate from any post-processing you've
> done for visualization purposes.
> 
> > I cant even use tpbconv command because trjconv
> > writes a xtc file and I need a trr file for my next run?
> 
> First, trjconv will write whatever trajectory file format you ask for, and
> this behaviour is common to all GROMACS tools. Second, you should be using
> the .trr output of the last mdrun to prepare the input for the
> continuations, and not the results of post-processing that output.
> 
> Mark
> 
> ___
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RE: [gmx-users] problem in bilayer simulation

[pragya chohan]

I think you misunderstood my reply. 
I understood that it is a periodic boundry condition problem and used trjconv. 
But it writes a trajectory file. How do I make a gro file to input it into next 
run? I cant even use tpbconv command because trjconv writes a xtc file and I 
need a trr file for my next run?


> Date: Mon, 31 Dec 2007 08:17:15 +1100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] problem in bilayer simulation
> 
> pragya chohan wrote:
> > Dear Users
> > I am doing membrane simulation alternating nvt and npt during production 
> > run. After 1250 ps the water from upper leaflet goes towards the lower 
> > leaflet and a very thin layer of water remains in the upper leaflet. Is 
> > it a common occurance or am I doing some mistake?
> 
> Probably you are observing an artefact of periodic boundary conditions - 
> see http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions for 
> advice here.
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] problem in bilayer simulation

[pragya chohan]

can you please suggest what should i do? I have pbc = xyz in my md.mdp> Date: 
Mon, 31 Dec 2007 08:17:15 +1100> From: [EMAIL PROTECTED]> To: 
gmx-users@gromacs.org> Subject: Re: [gmx-users] problem in bilayer simulation> 
> pragya chohan wrote:> > Dear Users> > I am doing membrane simulation 
alternating nvt and npt during production > > run. After 1250 ps the water from 
upper leaflet goes towards the lower > > leaflet and a very thin layer of water 
remains in the upper leaflet. Is > > it a common occurance or am I doing some 
mistake?> > Probably you are observing an artefact of periodic boundary 
conditions - > see 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions for > advice 
here.> > Mark> ___> gmx-users 
mailing list gmx-users@gromacs.org> 
http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at 
http://www.gromacs.org/search before posting!> Please don't post (un)subscribe 
requests to the list. Use the > www interface or send it to [EMAIL PROTECTED]> 
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[gmx-users] problem in bilayer simulation

[pragya chohan]

Dear Users
I am doing membrane simulation alternating nvt and npt during production run. 
After 1250 ps the water from upper leaflet goes towards the lower leaflet and a 
very thin layer of water remains in the upper leaflet. Is it a common occurance 
or am I doing some mistake?
Please help
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RE: [gmx-users] Segmentation fault

[pragya chohan]

hi
generally sementation fault occurs due to bad contacts in the system. As 
suggested by Mark see if the log file lists atom which have the problem.

> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Date: Sat, 29 Dec 2007 17:09:10 +0300
> Subject: [gmx-users] Segmentation fault
> 
> Hello,
> 
> I'm getting some problems about segmentation fault. I'm doing a protein 
> simulation during 20 ns on a water cubic box with a total of 23000 atoms.  
> I'm using the TIP3P water model at 300 K. Interestingly, when I use the 
> Berendsen barostat for pressure coupling, I've got a segmentation fault about 
> 1 ns of trajectory. When I don't use it the simulation extends untill 10 ns, 
> but the fault also occurs. Could it be some problem with memory limitation of 
> the computer? I'm using a cluster to run the simulations, and I'm trying to 
> check the memory capacity of the node that I've used.
> Besides, the message that I've seen is something like that:
> Step #number of the step and time mdrun -v -deffnm run   Segmentation 
> fault
> 
> Thank so much for the help and happy new year
> 
> Marcelo
> 
> 
> Marcelo Müller dos Santos, Ph.D. student
> Laboratorio de Tecnologia Enzimatica e Biocatalise
> Departamento de Bioquimica e Biologia Molecular, Setor de Ciencias 
> Biologicas, Centro Politecnico, Jardim da Américas, Curitiba - PR, Caixa 
> Postal: 190-46, CEP: 81531-990
> Phone: (+55) 41 3361-1658
> Fax: (+55) 41 3266-2042
> 
> Notícias direto do New York Times, gols do Lance, videocassetadas e muitos 
> outros vídeos no MSN Videos! Confira já!

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[gmx-users] deleted edr file

[pragya chohan]

Dear users
I by mistake deleted the edr file generated from production run. Is there any 
way to recover or generate the edr file again?
 
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RE: [gmx-users] insert protein in membrane again

[pragya chohan]

Did u match their box size before doing the genbox?
You could also get this error if you manually deleted that residue(s) from your 
gro file.

> Date: Tue, 18 Dec 2007 15:29:08 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] insert protein in membrane again
> 
> Hi again,
> 
> As I use genbox with my .gro file holding the protein and my .gro file
> containing the membrane I get the error message:
> 
> Fatal error: Invalid line in protein.gro for atom 2296:
> 
> There is no atom 2296 in protein.gro...
> 
> I must be missing something?
> 
> /Magnus
> 
> 
> -- 
> Magnus Andersson
> 
> Chalmers University of Technology
> Dept of Chemistry and Biological Engineering
> Email: [EMAIL PROTECTED]
> Homepage:  http://www.csb.gu.se/neutze/
> Phone: +46 (0)31-786 3917
> Fax: +46 (0)31-786 3910
> Lundberg Laboratory
> Medicinaregatan 9e
> SE-413 90 Göteborg
> Sweden
> 
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RE: [gmx-users] problem with npt

[pragya chohan]

ya i removed every water molecule that entered the bilayers. after pr should i 
do nvt before doing npt? i am doing position restrain also under npt.> Date: 
Mon, 17 Dec 2007 11:27:01 +0200> From: [EMAIL PROTECTED]> To: 
gmx-users@gromacs.org> Subject: Re: [gmx-users] problem with npt> > Hi,> have 
you checked if there is no water inside the membrane after the> use of genbox?> 
> On Dec 16, 2007 1:35 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:> > pragya 
chohan wrote:> > >> > > i started with the lipid coordinates from peter 
tieleman and removed the> > > water. then i added water by genbox.> > > I did 
energy minimization followed by position restrain, which I removed> > > 
gradually. all of it was done under npt. I carried out npt for 250> > > ps. 
During the next 250 ps npt run the bilayers separated and deformed.> >> > 
Usually NVT to get the temperature right before relaxing to NPT to let> > the 
density equilibrate can be good idea. Look at how much your box> > changed size 
during your NPT to see if this effect is causing problems.> >> >> > Mark> > 
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[gmx-users] membrane protein

[pragya chohan]

Dear User
I am starting a membrane simulation. Is it advisablr to complete all runs in 
npt or nvt?
Pragya Chohan
 
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RE: [gmx-users] coupling to water bath

[pragya chohan]

thanks its done. Please read my mail on problem with npt.> Date: Sun, 16 Dec 
2007 21:50:33 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> 
Subject: Re: [gmx-users] coupling to water bath> > pragya chohan wrote:> > how 
can we do that?> > The same way you make any index file - see > 
http://wiki.gromacs.org/index.php/Index_File> > Mark> 
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RE: [gmx-users] coupling to water bath

[pragya chohan]

how can we do that?> Date: Sun, 16 Dec 2007 19:55:30 +1100> From: [EMAIL 
PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] coupling to 
water bath> > pragya chohan wrote:> > Dear Users> > I have a system in of 
protein with in bound chlorine ion. I also added > > Na ion to the system to 
neutralize charge on system. I have to couple > > the system to water bath. can 
i couple protein chlorine and Na together > > and solvent separately? or should 
i couple protein and chlorine together > > and solvent and na together?> > 
Don't use T-coupling groups that might have molecules isolated inside > regions 
filled by other T-coupling groups. That won't be numerically stable.> > > I the 
later case -n option would take in 2 index files. then what should > > I do?> > 
You can make both groups inside the one index file.> > Mark> 
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[gmx-users] coupling to water bath

[pragya chohan]

Dear Users
I have a system in of protein with in bound chlorine ion. I also added Na ion 
to the system to neutralize charge on system. I have to couple the system to 
water bath. can i couple protein chlorine and Na together and solvent 
separately? or should i couple protein and chlorine together and solvent and na 
together?
I the later case -n option would take in 2 index files. then what should I do?
Thanks in advance
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RE: [gmx-users] problem with npt

[pragya chohan]

i started with the lipid coordinates from peter tieleman and removed the water. 
then i added water by genbox.
I did energy minimization followed by position restrain, which I removed 
gradually. all of it was done under npt. I carried out npt for 250 ps. During 
the next 250 ps npt run the bilayers separated and deformed. > Date: Sat, 15 
Dec 2007 09:53:06 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> 
Subject: RE: [gmx-users] problem with npt> > Quoting pragya chohan <[EMAIL 
PROTECTED]>:> > >> >> > I wrote yes to generate velocity. Can that be a reason 
for the problem? Since> > I am doing membrane simulation it is advised to do 
production runs in npt> > thats the only other difference.> > I think what Mark 
was asking for was a bit more detail on how you put your> system together. It 
would be helpful to know (step by step) what you did, as> that may highlight a 
problem. Also, what do you define as "deformed very> much?" Some fluctuations 
are to be expected, and 250 ps is a relatively short> time frame. In some of my 
bilayer simulations, the lipids look quite strange> under NVT, but after a 
nanosecond or two or NPT they even out and behave> normally.> > -Justin> > > 
> > > Date: Sat, 15 Dec 2007 06:03:27 
+1100> > > From: [EMAIL PROTECTED]> > > To: gmx-users@gromacs.org> > > Subject: 
Re: [gmx-users] problem with npt> > >> > > pragya chohan wrote:> > > >> > > > 
thanks for your help.> > > > My system ran fine for 250 ps but later the 
bilayer deformed very much.> > >> > > What was your system preparation protocol 
- i.e. minimization and> > > equilibration? See> > > 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation> > >> > > Mark> 
> > ___> > > gmx-users mailing list 
gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users> > 
> Please search the archive at http://www.gromacs.org/search before posting!> > 
> Please don't post (un)subscribe requests to the list. Use the> > > www 
interface or send it to [EMAIL PROTECTED]> > > Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php> >> > 
_> > Post free 
property ads on Yello Classifieds now! www.yello.in> >> 
http://ss1.richmedia.in/recurl.asp?pid=220___>
 > gmx-users mailing list gmx-users@gromacs.org> > 
http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive 
at http://www.gromacs.org/search before posting!> > Please don't post 
(un)subscribe requests to the list. Use the> > www interface or send it to 
[EMAIL PROTECTED]> > Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php> >> > > > 
> > Justin A. Lemkul> Graduate Research 
Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL 
PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> 
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RE: [gmx-users] problem with npt

[pragya chohan]

I wrote yes to generate velocity. Can that be a reason for the problem? Since I 
am doing membrane simulation it is advised to do production runs in npt thats 
the only other difference.

> Date: Sat, 15 Dec 2007 06:03:27 +1100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] problem with npt
> 
> pragya chohan wrote:
> > 
> > thanks for your help.
> > My system ran fine for 250 ps but later the bilayer deformed very much.
> 
> What was your system preparation protocol - i.e. minimization and 
> equilibration? See 
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
> 
> Mark
> ___
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RE: [gmx-users] problem with npt

[pragya chohan]

thanks for your help.
My system ran fine for 250 ps but later the bilayer deformed very much.
my mdp is
integrator  =  md
dt  =  0.002; ps !
nsteps  =  125000   ; total 100 ps.
nstcomm =  1
nstxout =  250
nstenergy   =  100
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  cut-off
rcoulomb=  1.0
rvdw=  0.9
rlist   =  0.9
; Berendsen temperature coupling is on in two groups
; aniisotropic pressure coupling is now on
Tcoupl  =  nose-hoover
Pcoupl  =  Parrinello-Rahman
pcoupltype  =  semiisotropic
tc-grps =  POPC SOL
tau_t   =  0.5  0.5
ref_t   =  323  323
ref_p   =  11
tau_p   =  10   10
compressibility =  4.5e-5   4.5e-5
; Energy monitoring
energygrps  =  POPC  SOL

Can anyone help?


> Date: Wed, 5 Dec 2007 11:27:40 +1100
> Subject: Re: [gmx-users] problem with npt
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> 
> >
> > Dear users
> > I was tyring to run an npt simulation of membrane. My mdp is:
> 
> > As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/
> > i am using Parrinello-Rahman instead of berendsen. The problem is that the
> > box size is getting reduced to 9.99448 9.99448 9.25077 from 10.0 10.0 10.0
> > and water is compressing the bilayer.
> 
> This is the purpose of equilibration with NPT - to fix density issues. The
> contraction in Z suggests that your membrane is insufficiently dense in
> that direction, or has some vacuum pockets. That's not a problem in itself
> so long as you equilibrate long enough. Berendsen P-coupling will likely
> do the same thing.
> 
> > I also tried anisotropic coupling
> > pcoupltype = anisotropic
> > tc-grps = POPC SOL
> > tau_t = 0.1 0.1
> > ref_t = 300 300
> > ref_p = 1 1 1 0 0 0
> > tau_p = 10
> > compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
> > This time my box size is reducing to 9.99065 9.99717 9.17646.
> > I cant figure out the problem. Any help will be appreciated.
> 
> This suggests the same non-problem exists.
> 
> Mark
> 
> ___
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[gmx-users] problem with npt

[pragya chohan]

Dear users
I was tyring to run an npt simulation of membrane. My mdp is:
 
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 100 ps.
nstcomm = 1
nstxout = 250
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = cut-off
; Berendsen temperature coupling is on in two groups
; aniisotropic pressure coupling is now on
Tcoupl = berendsen
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tc-grps = POPC SOL
tau_t = 0.1 0.1
ref_t = 300 300
ref_p = 1 1
tau_p = 10
compressibility = 4.5e-5 4.5e-5
; Energy monitoring
energygrps = POPC SOL
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
comm_grps = POPC SOL
 
As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/ i am 
using Parrinello-Rahman instead of berendsen. The problem is that the box size 
is getting reduced to 9.99448 9.99448 9.25077 from 10.0 10.0 10.0 and water is 
compressing the bilayer.
I also tried anisotropic coupling
pcoupltype = anisotropic
tc-grps = POPC SOL
tau_t = 0.1 0.1
ref_t = 300 300
ref_p = 1 1 1 0 0 0
tau_p = 10
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
This time my box size is reducing to 9.99065 9.99717 9.17646.
I cant figure out the problem. Any help will be appreciated.
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[gmx-users] asymmetric distribution of water

[pragya chohan]

hi ... i want to start a simulation with asymmetric distribution of water on 
the bilayer (upper leaftlet having more and lower one less). has anyone ever 
encountered a paper with such a simulation. Is it possible?
Thanks for any help
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[gmx-users] commanf for wrapping

[pragya chohan]

hi  i want to wrap my lipid in water... which centres the lipid in water. I 
know a command for this in amber (iwrap ). Is there a corresponding command in 
gromacs
thanks for your help
Pragya Chohan

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RE: [gmx-users] position restrain

[pragya chohan]

Thanks for your help. My simulation ran with your idea.

> Date: Thu, 15 Nov 2007 13:34:40 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restrain
> 
> If you read the documentation for genpr, it tells you that it will only 
> generate
> a position restraint file for the first molecule, so grompp is telling you 
> that
> only the protein is being restrained, which is what you should expect.  If you
> really insist on restraining the water molecules, try reading about the
> freezegrps options for your .mdp file, but doing so will typically cause
> problems if you are using pressure coupling.
> 
> -Justin
> 
> Quoting pragya chohan <[EMAIL PROTECTED]>:
> 
> >
> > hi
> > I have a system of protein, popc,water and Cl ions. I want to position
> > restrain protein and water as without position restrain water is going into
> > the membrane . So I made a group of protein and water together using 
> > make_ndx
> > and then genpr. When i ran grompp i got the following error:
> >
> > ---
> > Program grompp, VERSION 3.3
> > Source code file: toppush.c, line: 1108
> >
> > Fatal error:
> > [ file "posre1.itp", line 582 ]:
> >  Atom index (5362) in position_restraints out of bounds (1-577)
> >
> > The commands i used are:
> > make_ndx -f em_dpt_popc.gro -o
> >  0 System  : 12663 atoms
> >   1 Protein :   577 atoms
> >   2 Protein-H   :   456 atoms
> >   3 C-alpha :59 atoms
> >   4 Backbone:   177 atoms
> >   5 MainChain   :   237 atoms
> >   6 MainChain+Cb:   294 atoms
> >   7 MainChain+H :   296 atoms
> >   8 SideChain   :   281 atoms
> >   9 SideChain-H :   219 atoms
> >  10 Prot-Masses :   577 atoms
> >  11 Non-Protein : 12086 atoms
> >  12 POPC:  4784 atoms
> >  13 SOL :  7299 atoms
> >  14 Cl  : 3 atoms
> >  15 Other   : 12086 atoms
> >
> >  nr : group   !   'name' nr name   'splitch' nrEnter: list groups
> >  'a': atom&   'del' nr 'splitres' nr   'l': list residues
> >  't': atom type   |   'keep' nr'splitat' nr'h': help
> >  'r': residue 'res' nr 'chain' char
> >  "name": group'case': case sensitive   'q': save and quit
> >
> > > 1|13
> >
> > Copied index group 1 'Protein'
> > Copied index group 13 'SOL'
> > Merged two groups with OR: 577 7299 -> 7876
> >
> >  16 Protein_SOL :  7876 atoms
> >
> > > q
> >
> > genpr -f em_dpt_popc.gro -o posre1 -n index.ndx
> >
> > Group16 ( Protein_SOL) has  7876 elements
> > Select a group: 16
> > Selected 16: 'Protein_SOL'
> >
> > grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o
> > pr_dpt_popc
> >
> > What is the best way to do this? Please suggest.
> > _
> > Check out some new online services at Windows Live Ideas—so new they haven’t
> > even been officially released yet.
> >
> http://www.msnspecials.in/windowslive/___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
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> >
> 
> 
> 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> 
> 
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[gmx-users] pressure coupling for bilayers

[pragya chohan]

hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best 
pcoupletype to use. I have seen some posts on gmx user group advising 
anisotriopic type with 
tau_p 5.0 ps
cpmpressibility: 4.5e-5 4.5e-5 4.5e-5 0.0  0.0 0.0

Another suggestion is welcome.
Thanks in advance
Pragya

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[gmx-users] position restrain

[pragya chohan]

hi 
I have a system of protein, popc,water and Cl ions. I want to position restrain 
protein and water as without position restrain water is going into the membrane 
. So I made a group of protein and water together using make_ndx and then 
genpr. When i ran grompp i got the following error:

---
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file "posre1.itp", line 582 ]:
 Atom index (5362) in position_restraints out of bounds (1-577)

The commands i used are:
make_ndx -f em_dpt_popc.gro -o
 0 System  : 12663 atoms
  1 Protein :   577 atoms
  2 Protein-H   :   456 atoms
  3 C-alpha :59 atoms
  4 Backbone:   177 atoms
  5 MainChain   :   237 atoms
  6 MainChain+Cb:   294 atoms
  7 MainChain+H :   296 atoms
  8 SideChain   :   281 atoms
  9 SideChain-H :   219 atoms
 10 Prot-Masses :   577 atoms
 11 Non-Protein : 12086 atoms
 12 POPC:  4784 atoms
 13 SOL :  7299 atoms
 14 Cl  : 3 atoms
 15 Other   : 12086 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit

> 1|13

Copied index group 1 'Protein'
Copied index group 13 'SOL'
Merged two groups with OR: 577 7299 -> 7876

 16 Protein_SOL :  7876 atoms

> q

genpr -f em_dpt_popc.gro -o posre1 -n index.ndx

Group16 ( Protein_SOL) has  7876 elements
Select a group: 16
Selected 16: 'Protein_SOL'

grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o 
pr_dpt_popc

What is the best way to do this? Please suggest.
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RE: [gmx-users] mdrun error

[pragya chohan]

hi 
i tried to run the simulation with single alamethicin molecule but i am getting 
the same error as i was getting earlier.
Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is 
larger than the 1-4 table size 1.000 nm.
I used the command 
 $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro 
my pdb file at 164 to 169 is:
ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00
ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00
ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00
ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00
ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00
ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00.
This is occuring at the start of equillibration step . I have not done any 
simulation as yet. 
I also tried pre-equillibrating the protein and directly simulating by restrain 
but that also is not working.

I cannot figure out the problem. Please help

at Windows Live Ideas—so new they>>> haven’t even been officially released 
yet. 
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Virginia>>> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080>> 
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=>> 
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=>> Justin A.>>> 
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Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> 
= 
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= Justin A. 
Lemkul>> Graduate Research Assistant>> Department of Biochemistry>> Virginia 
Tech>> Blacksburg, VA>> [EMAIL PROTECTED] | (540) 231-9080>> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ 
= 
=>> Justin A. Lemkul> 
Graduate Research Assistant> Department of Biochemistry> Virginia Tech> 
Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>> 
=> 
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[gmx-users] (no subject)

[pragya chohan]

hi.
Has anyone used inflategro provided on 
"http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis";. I am having 
problem in using it. When I enter my gro file no lipids are removed. Please 
reply.
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RE: [gmx-users] mdrun error

[pragya chohan]

Hi justin 
I placed POPC membrane in a box too of same dimension as the box of alamethicin 
and centred it too so that alamethicin is placed correctly in the membrane. 
I am attaching the pdb please have a look.Any help would be appreciated
 
Pragya



> Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya 
> chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am 
> generating the starting structure through> > genbox.> > I added popc as 
> solvent around alamethicin after aligning alamethicin in a> > box and 
> centering it in the box and followed same procedure for popc also. Do> > you 
> have any better way?> >> > In theory, that should work just fine, but I don't 
> understand what you mean by> "followed the same procedure for popc." What did 
> you do there? The first part> should be all you need (alamethicin in the box, 
> solvated with popc).> > Alternatively, you can use make_hole.pl or the 
> inflategro script available> through Peter Tieleman's site:> > 
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis> > -Justin> > >> 
> >> > > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:> > 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since> > 
> alamethicin works on its own, it suggests to me that the introduction of>> > 
> alamethicin into POPC is what's causing the problem, and judging by the>> > 
> enormous potential energies and forces, it appears to be bad 
> contacts/atomic>> > overlap (at least, that's been the cause of problems in 
> my experience). How>> > are you generating your starting structure?> > 
> -Justin> > >> > Thanks for> > your help. I figured the problem out but am 
> getting an error> > again. I have> > alamethicin in popc and water. Since 
> alamethicin has some non> > standard> > residue i made topology file in text 
> editor and ran mdrun with only> >> > alamethicin. It went fine. But when i am 
> tring to minimize alamethicin in> >> > popc mdrum probably does not recognize 
> the starting of second chain and> > gives> > me following error:> >> > 
> Warning: 1-4 interaction between 164 and> > 169 at distance 3.430 which is> > 
> larger than the 1-4 table size 1.000 nm> >> > These are ignored for the rest 
> of the simulation> > This usually means your> > system is exploding,> > if 
> not, you should increase table-extension in your> > mdp file> > Step= 1, 
> Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,> > atom=> > 2441> > 
> Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=> > 1.82388e+08, atom=> > 
> 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09> > Fmax= 7.44135e+07, 
> atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09> > Fmax= 
> 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09> > 
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09> 
> > Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 
> 1.81606e+09> > Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, 
> Epot= 1.79660e+09> > Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 
> nm, Epot= 1.78793e+09> > Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 
> 5.2e-02 nm, Epot= 1.77532e+09> > Fmax= 7.54157e+06, atom=> > 12539> > Step= 
> 11, Dmax= 6.2e-02 nm, Epot=> > 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> 
> > Step= 12, Dmax= 7.4e-02 nm,> > Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> 
> > 12539> > Step= 13, Dmax=> > 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 
> 7.11508e+06, atom=> > 12539> > Wrote pdb> > files with previous and current 
> coordinates> >> > Back Off! I just backed up> > step13.pdb to 
> ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to> > 
> ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> 
> >>> > > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 
> 35.170> > 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > 
> ATOM 166 CX> > PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 
> 37.940 49.350> > 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 
> 1

RE: [gmx-users] mdrun error

[pragya chohan]

Thanks Justin for your reply. I am generating the starting structure through 
genbox.
I added popc as solvent around alamethicin after aligning alamethicin in a box 
and centering it in the box and followed same procedure for popc also. Do you 
have any better way?



> Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since 
> alamethicin works on its own, it suggests to me that the introduction of> 
> alamethicin into POPC is what's causing the problem, and judging by the> 
> enormous potential energies and forces, it appears to be bad contacts/atomic> 
> overlap (at least, that's been the cause of problems in my experience). How> 
> are you generating your starting structure?> > -Justin> > >> > Thanks for 
> your help. I figured the problem out but am getting an error> > again. I have 
> alamethicin in popc and water. Since alamethicin has some non> > standard 
> residue i made topology file in text editor and ran mdrun with only> > 
> alamethicin. It went fine. But when i am tring to minimize alamethicin in> > 
> popc mdrum probably does not recognize the starting of second chain and 
> gives> > me following error:> >> > Warning: 1-4 interaction between 164 and 
> 169 at distance 3.430 which is> > larger than the 1-4 table size 1.000 nm> > 
> These are ignored for the rest of the simulation> > This usually means your 
> system is exploding,> > if not, you should increase table-extension in your 
> mdp file> > Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, 
> atom=> > 2441> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 
> 1.82388e+08, atom=> > 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 
> Fmax= 7.44135e+07, atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 
> Fmax= 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 
> Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 
> Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 
> Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 
> Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 
> Fmax= 7.54157e+06, atom=> > 12539> > Step= 11, Dmax= 6.2e-02 nm, Epot= 
> 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> > Step= 12, Dmax= 7.4e-02 nm, 
> Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> > 12539> > Step= 13, Dmax= 
> 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom=> > 12539> > Wrote pdb 
> files with previous and current coordinates> >> > Back Off! I just backed up 
> step13.pdb to ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to 
> ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> >> 
> > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 35.170 
> 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > ATOM 166 CX 
> PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 37.940 49.350 
> 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00> > ATOM 
> 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00> >> > I think it is not 
> recognising different chain. Am i right? Please help me.> > 
> _> > Check 
> out some new online services at Windows Live Ideas—so new they haven’t> > 
> even been officially released yet.> >> 
> http://www.msnspecials.in/windowslive/___>
>  > gmx-users mailing list gmx-users@gromacs.org> > 
> http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the 
> archive at http://www.gromacs.org/search before posting!> > Please don't post 
> (un)subscribe requests to the list. Use the> > www interface or send it to 
> [EMAIL PROTECTED]> > Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php> >> > > > 
> => > Justin A. 
> Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia 
> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> => 
> ___> gmx-users mailing list 
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RE: [gmx-users] mdrun error

[pragya chohan]

> Date: Fri, 9 Nov 2007 09:01:48 -0500> 
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] 
mdrun error>> Check out the wiki at:>> 
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings>> Alternatively, search 
the list for some of my posts from around a year ago - NVT> and minimization of 
a lipid bilayer (or search for my name, they should come up> as well). I 
suspect you have bad contacts in your starting structure.>> -Justin>> Quoting 
pragya chohan :>>>>> hi i am trying to run mdrun for protein in membrane 
system. When i run mdrun>> i get a warning>>>> Step -2, time -0.002 (ps) LINCS 
WARNING>> relative constraint deviation after LINCS:>> max 2.144082 (between 
atoms 12433 and 12434) rms 0.216090>> bonds that rotated more than 30 
degrees:>> atom 1 atom 2 angle previous, current, constraint length>> 11761 
11762 90.0 0.1633 0.2387 0.1000>> 11929 11930 31.7 0.1633 0.1000 0.1000>> 12097 
12098 90.0 0.1632 0.1041 0.1000>> 12265 12266 90.0 0.1633 0.2266 0.1000>> 12433 
12434 90.0 0.1633 0.3144 0.1000>> starting mdrun 'alamethicin in popc'>> 500 
steps, 0.5 ps.>>>> Warning: 1-4 interaction between 115 and 136 at distance 
1.144 which is>> larger t>> han the 1-4 table size 1.000 nm>> These are ignored 
for the rest of the simulation>> This usually means your system is exploding,>> 
if not, you should increase table-extension in your mdp file>>>> Step 0, time 0 
(ps) LINCS WARNING>> relative constraint deviation after LINCS:>> max inf 
(between atoms 12007 and 12008) rms inf>> bonds that rotated more than 30 
degrees:>> atom 1 atom 2 angle previous, current, constraint length>> 11619 
11620 90.0 0.1000 0.1411 0.1000>> 11633 11634 90.0 0.1000 13155507200. 
0.1000>> 11640 11641 90.0 0.1000 0.1214 0.1000>> .>> 12619 12620 90.0 
0.1080 0.1447 0.1080>> Wrote pdb files with previous and current coordinates>> 
step 0Segmentation fault>> I am using shake in my mdp file. I want to restrain 
water.>>>> my mdp file is:>> title = popc128a>> integrator = md>> define = 
-DFLEX_SPC>> dt = 0.001>> nsteps = 500>> nstxout = 500>> ns_type = grid>> pbc = 
xyz>> constraints = hbonds>> constraints_algorithm= shake>> coulombtype = PME>> 
vdwtype = cut-off>> rcoloumb = 1.0>> nstlist = 10.0>> Tcoupl = no>> pcoupl = 
no>> compressibility = 4.5e-5>> gen_temp = 300>> gen_vel = no>> Please help.>> 
Thanks in advance.>> 
_>> Check out 
some new online services at Windows Live Ideas—so new they haven’t>> even been 
officially released yet.>>> 
http://www.msnspecials.in/windowslive/___>>
 gmx-users mailing list gmx-users@gromacs.org>> 
http://www.gromacs.org/mailman/listinfo/gmx-users>> Please search the archive 
at http://www.gromacs.org/search before posting!>> Please don't post 
(un)subscribe requests to the list. Use the>> www interface or send it to 
[EMAIL PROTECTED]>> Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php>>>>>> 
=>> Justin A. Lemkul> 
Graduate Research Assistant> Department of Biochemistry> Virginia Tech> 
Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>> 
=> 
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Thanks for your help. I figured the problem out but am getting an error again. 
I have alamethicin in popc and water. Since alamethicin has some non standard 
residue i made topology file in text editor and ran mdrun with only 
alamethicin. It went fine. But when i am tring to minimize alamethicin in popc 
mdrum probably does not recognize the starting of second chain and gives me 
following error:

Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger 
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase tab

[gmx-users] mdrun error

[pragya chohan]

hi i am trying to run mdrun for protein in membrane system. When i run mdrun i 
get a warning

Step -2, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.144082 (between atoms 12433 and 12434) rms 0.216090
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11761  11762   90.00.1633   0.2387  0.1000
  11929  11930   31.70.1633   0.1000  0.1000
  12097  12098   90.00.1632   0.1041  0.1000
  12265  12266   90.00.1633   0.2266  0.1000
  12433  12434   90.00.1633   0.3144  0.1000
starting mdrun 'alamethicin in popc'
500 steps,  0.5 ps.

Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t
han the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 12007 and 12008) rms inf
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11619  11620   90.00.1000   0.1411  0.1000
  11633  11634   90.00.1000 13155507200.  0.1000
  11640  11641   90.00.1000   0.1214  0.1000
.
  12619  12620   90.00.1080   0.1447  0.1080
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
I am using shake in my mdp file. I want to restrain water.

my mdp file is:
title= popc128a
integrator   = md
define   = -DFLEX_SPC
dt   = 0.001
nsteps   = 500
nstxout  = 500
ns_type  = grid
pbc  = xyz
constraints  = hbonds
constraints_algorithm= shake
coulombtype  = PME
vdwtype  = cut-off
rcoloumb = 1.0
nstlist  = 10.0
Tcoupl   = no
pcoupl   = no
compressibility  = 4.5e-5
gen_temp = 300
gen_vel  = no
Please help.
Thanks in advance.
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RE: [gmx-users] installation error

[pragya chohan]

> Date: Thu, 8 Nov 2007 12:35:29 +1100> 
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] 
installation error>> pragya chohan wrote:>> hi>> I had installed make_hole 
utility earlier but when i tried to run:>> make_hole.pl -f box_popc.pdb -o 
hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8>> I get :>> bash: 
make_hole.pl: command not found.>> So make-hole.pl, or something in its shebang 
line is probably not in> your path.>>> I tried reinstalling it by ./configure 
which completed successfully but when i ran make command i get the following 
error:>> This is the output from configuring GROMACS, not make_hole.pl>> In 
any case, you should do "make distclean" between runs of configure> with 
different settings, and/or system configuration.>> Mark> 
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Thanks for your reply.
when i run make distclean i get following error:

make[2]: *** No rule to make target `.deps/wnblist.Plo'.  Stop.
make[2]: Leaving directory 
`/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/mdlib'
make[1]: *** [distclean-recursive] Error 1
make[1]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src'
make: *** [distclean-recursive] Error 1


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[gmx-users] installation error

[pragya chohan]

hi
I had installed make_hole utility earlier but when i tried to run:
make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 
51.5 -cy 51.8
I get :
bash: make_hole.pl: command not found.
I tried reinstalling it by ./configure which completed successfully but when i 
ran make command i get the following error:

nonbonded.c:272: error: `esolSPC' undeclared (first use in this function)
nonbonded.c:272: error: (Each undeclared identifier is reported only once
nonbonded.c:272: error: for each function it appears in.)
nonbonded.c:276: error: `esolTIP4P' undeclared (first use in this function)
nonbonded.c:472: error: `enlistWATER' undeclared (first use in this function)
nonbonded.c:476: error: `enlistWATERWATER' undeclared (first use in this 
function)
nonbonded.c: In function `do_nonbonded14':
nonbonded.c:542: error: `eelRF_NEC' undeclared (first use in this function)
nonbonded.c:569: error: `epbcFULL' undeclared (first use in this function)
make[5]: *** [nonbonded.lo] Error 1
make[5]: Leaving directory 
`/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib/nonbonded'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory 
`/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib/nonbonded'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory 
`/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src'
make: *** [all-recursive] Error 1
 Please help me
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RE: [gmx-users] alamethicin error

[pragya chohan]

> Date: Fri, 2 Nov 2007 09:39:36 +1100> 
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] 
alamethicin error>> pragya chohan wrote:>> i got this error "atom C not found 
in residue 84PHL while combining tdb and rtp" when i tried to do pdb2gmx>> the 
commamd used is:>> pdb2gmx -ter -ff gmx -f alamethicin.pdb -o alamethicin.gro 
-p ala.top>> There's a warning given by pdb2gmx about this forcefield. You 
would do> well to read it.>>> Select N-terminus type (start)>> 0: NH3+>> 1: 
NH2>> 2: None>> 2>> N-terminus: None>> Select C-terminus type (end)>> 0: COO->> 
1: COOH>> 2: None>> 1>> C-terminus: COOH>> even if i use option 0 i get an the 
same error. But if i ued option 2 in C-terminali get :>> Atom C not found in 
residue 21 while adding improper... which is also PHL>> 84PHL is>> ATOM 655 N 
PHL 84 42.380 33.130 47.420 1.00 0.00>> ATOM 656 H PHL 84 41.620 33.340 46.800 
1.00 0.00>> ATOM 657 CA PHL 84 43.050 34.310 47.980 1.00 0.00>> ATOM 658 CB PHL 
84 43.960 34.910 46.910 1.00 0.00>> ATOM 659 CG PHL 84 45.060 33.960 46.410 
1.00 0.00>> ATOM 660 CD1 PHL 84 46.080 33.540 47.290 1.00 0.00>> ATOM 661 HD1 
PHL 84 46.090 33.860 48.320 1.00 0.00>> ATOM 662 CD2 PHL 84 45.040 33.520 
45.070 1.00 0.00>> ATOM 663 HD2 PHL 84 44.280 33.880 44.390 1.00 0.00>> ATOM 
664 CE1 PHL 84 47.080 32.660 46.830 1.00 0.00>> ATOM 665 HE1 PHL 84 47.870 
32.330 47.480 1.00 0.00>> ATOM 666 CE2 PHL 84 46.040 32.650 44.600 1.00 0.00>> 
ATOM 667 HE2 PHL 84 46.050 32.350 43.570 1.00 0.00>> ATOM 668 CZ PHL 84 47.050 
32.220 45.490 1.00 0.00>> ATOM 669 HZ PHL 84 47.830 31.570 45.140 1.00 0.00>> 
ATOM 670 CX PHL 84 41.990 35.310 48.450 1.00 0.00>> ATOM 671 OY PHL 84 40.950 
34.570 49.110 1.00 0.00>> ATOM 672 HY PHL 84 40.110 35.090 49.220 1.00 0.00>> 
So, what important part of an amino *acid* residue is missing from this> 
fragment?>> Mark> ___> gmx-users 
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Thanks Mark. The C terminal does not have a -COOH group at the end but rater 
has a -OH group PHL is actually PHENYLALANINOL.
But when i put option 2 whn prompted for 
select C-terminus type (end)>> 0: COO->> 1: COOH>> 2: None 
 i still get an error Atom C not found in residue 21 while adding improper.
I checked the naming in ffgmx.rtp but everything seems to be fine. 
Thanks for your help.

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RE: [gmx-users] gramicidin A

[pragya chohan]

> Date: Sat, 3 Nov 2007 19:23:32 +1100> 
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] 
gramicidin A>> pragya chohan wrote:>> hi>> I was trying to run pdb2gmx command 
for gramicidin and noticed it has some D-amino acids.>> D-amino acids are 
enantiomers of L-amino acids. Thus they're> topologically identical. So you can 
use the same topology for them,> unless your force field has an interaction 
that varies with chirality.> You know already whether your force field has one 
of them, right? If it> doesn't, then you can just change some names.>>> I 
generated .itp from prodrg server and included the above stated things in .rtp 
file. But again when i ran pdb2gmx i got the same error..>> Residue 'DLE' not 
found in residue topology database.>> See> 
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database>>
 You need to do some more work in understanding the purpose of running> 
pdb2gmx, the way of using an .itp file, and/or understanding the .rtp> file 
syntax. Check out http://wiki.gromacs.org/index.php/topology_file> and chapter 
5 of the GROMACS manual.>> Mark> 
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Thanks for your reply
I had already read the refered pages . I had made changes in the charge and 
improper dihedrals. But pdb2gmx doesnt seem to recognise those amino acids 
still. 
No i dont know if my force field if chiraliy sensitive. Neways my system also 
has Val in it.
The changes i made are
[ LEU ](ORIGINAL LEU)
 [ atoms ]
 N N  -0.280 0
 H H   0.280 0
CA   CH1   0.000 1
CB   CH2   0.000 2
CG   CH1   0.000 3
   CD1   CH3   0.000 4
   CD2   CH3   0.000 5
 C C   0.380 6
 O O  -0.380 6
 [ bonds ]
 N H
 NCA
CA C
 C O
-C N
CACB
CBCG
CG   CD1
CG   CD2
 [ impropers ]
 N-CCA H
-C   -CA N-O
CA N CCB
CG   CD2   CD1CB

[ DLE ](INCORPORATED DLE)
 [ atoms ]
 N N   0.815 0
 H H   0.041 0
CA   CH1   0.189 1
CB   CH2   0.000 2
CG   CH1   0.000 3
   CD1   CH3   0.000 4
   CD2   CH3   0.000 5
 C C   0.432 6
 O O  -0.559 6
 [ bonds ]
 N H
 NCA
CA C
 C O
-C N
CACB
CBCG
CG   CD1
Please help me.
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[gmx-users] gramicidin A

[pragya chohan]

hi 
I was trying to run pdb2gmx command for gramicidin and noticed it has some 
D-amino acids. Reading the earlier mail wjich states that:
It's not too difficult to add a new residue to the topology database. 
Have a look in the file ff.rtp, where  is the force field 
you are using.

You can probably copy most parts from a standard amino acid that is 
similar to your new one. There are three parts for each residue:

[atoms]
This section maps names found in the pdb file (col 1) to atom types (col 
2), charge (col 3) and charge groups (col 4). Try to have neutral charge 
groups.

[bonds]
Just define the connectivity in the residue. Names prepended with a dash 
("-") refer to atoms in the next residue, if present.

[impropers]
Define the improper dihedrals needed to maintain chirality of the molecule.


That's it - everything else like angles, normal dihedrals, and the 
actual parameters will be generated by pdb2gmx.

I generated .itp from prodrg server and included the above stated things in 
.rtp file. But again when i ran pdb2gmx i got the same error..
Residue 'DLE' not found in residue topology database.

What should i do? if anyone has topology file for gramicidin please send me 

Thanks in advance
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[gmx-users] alamethicin error

[pragya chohan]

i got this error "atom C not found in residue 84PHL while combining tdb and 
rtp" when i tried to do pdb2gmx
the commamd used is:
pdb2gmx -ter -ff gmx -f alamethicin.pdb -o alamethicin.gro -p ala.top
Select N-terminus type (start)
 0: NH3+
 1: NH2
 2: None
2
N-terminus: None
Select C-terminus type (end)
 0: COO-
 1: COOH
 2: None
1
C-terminus: COOH
even if i use option 0 i get an the same error. But if i ued option 2 in 
C-terminali get :
Atom C not found in residue 21 while adding improper... which is also PHL
84PHL is
ATOM655  N   PHL84  42.380  33.130  47.420  1.00  0.00
ATOM656  H   PHL84  41.620  33.340  46.800  1.00  0.00
ATOM657  CA  PHL84  43.050  34.310  47.980  1.00  0.00
ATOM658  CB  PHL84  43.960  34.910  46.910  1.00  0.00
ATOM659  CG  PHL84  45.060  33.960  46.410  1.00  0.00
ATOM660  CD1 PHL84  46.080  33.540  47.290  1.00  0.00
ATOM661  HD1 PHL84  46.090  33.860  48.320  1.00  0.00
ATOM662  CD2 PHL84  45.040  33.520  45.070  1.00  0.00
ATOM663  HD2 PHL84  44.280  33.880  44.390  1.00  0.00
ATOM664  CE1 PHL84  47.080  32.660  46.830  1.00  0.00
ATOM665  HE1 PHL84  47.870  32.330  47.480  1.00  0.00
ATOM666  CE2 PHL84  46.040  32.650  44.600  1.00  0.00
ATOM667  HE2 PHL84  46.050  32.350  43.570  1.00  0.00
ATOM668  CZ  PHL84  47.050  32.220  45.490  1.00  0.00
ATOM669  HZ  PHL84  47.830  31.570  45.140  1.00  0.00
ATOM670  CX  PHL84  41.990  35.310  48.450  1.00  0.00
ATOM671  OY  PHL84  40.950  34.570  49.110  1.00  0.00
ATOM672  HY  PHL84  40.110  35.090  49.220  1.00  0.00

pls help me
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[gmx-users] itp for alamethicin

[pragya chohan]

hi... i have to make an itp file for alamethicin  already tried prodrg2 but 
no success. pls suggest a way for making .itp file .. residue already 
defined in ffgmx.rtp. ...already read earlier query posted but could not find 
an ans.
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[gmx-users] grompp error for alamethicin

[pragya chohan]

hi ... when i run grompp i get an error " No such moleculetype Protein " ... i 
included itp for ACE and AIB after generating them from PRODRG2 server... my 
top file is :

; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "ace.itp"
#include "aib.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein 1

The command i m using is :

grompp -f 7eq_w.mdp -c ala.gro -p aquapo_grom.top -o alam.tpr

ala.gro is generated using editconf.
The .mdp file is

integrator   = md
define   = -DPOSRES -DFLEX_SPC
dt   = 0.002
nsteps   = 25000
nstxout  = 500
ns_type  = grid
pbc  = xyz
constraints  = hbonds
constraints_algorithm= shake
coulombtype  = PME
vdwtype  = cut-off
rcoloumb = 1.4

Tcoupl   = berendsen
pcoupl   = berendsen
tau_t= 0.1   0.1
tc_grps  = POPC  SOL
ref_t= 300   300
ref_p= 1.0
pcoupltype   = isotropic
compressibility  = 4.5e-5
gen_temp = 300

Pls reply as soon as possible

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[gmx-users] grompp error

[pragya chohan]

hi... i have been trying to do grompp for the following file but am getting 
this error:
There were 1 error(s) processing your inputWARNING 3 [file "popc.top", line 
32]:  7380 non-matching atom names  atom names from popc.top will be used  atom 
names from popc.pdb will be ignored
double-checking input for internal consistency...ERROR: The cut-off length is 
longer than half the shortest box vector or longer than the smallest box 
diagonal element. Increase the box size or decrease rlist.There were 3 warnings
The grompp command i am using is:
grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr
 
the inputs are:
 
popc.mdp
 
title= popc128aintegrator   = mddefine   = 
-DPOSRES -DFLEX_SPCdt   = 0.002nsteps   = 
25000nstxout  = 500ns_type  = gridpbc  
= xyzconstraints  = hbondsconstraints_algorithm= shakecoulombtype   
   = PMEvdwtype  = cut-offrcoloumb = 1.4
Tcoupl   = berendsenpcoupl   = berendsentau_t   
 = 0.1   0.1tc_grps  = POPC  SOLref_t= 
300   300ref_p= 1.0pcoupltype   = 
isotropiccompressibility  = 4.5e-5gen_temp = 300
popc.top
 
#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp"
#ifdef FLEX_SPC#include "flexspc.itp"#else#include "spc.itp"#endif
#ifdef POSRES_WATER; Position restraint for each water oxygen[ 
position_restraints ];  i funct   fcxfcyfcz   11   
1000   1000   1000#endif
; Include generic topology for ions#include "ions.itp"
#ifdef POSRES#include "lipid_posre.itp"#endif
[ system ]; NamePure DPPC bilayer with 128 lipids and 3655 water molecules
[ molecules ]; Compound#molsPOPC  128SOL   2460
 
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[gmx-users] simulation popc

[pragya chohan]

hi i m pragya, i found this article  i used ffG43a1 and got this error when 
ran grompp:
Atomtype 'CA' not found! . i m using popc128a.pdb from tieleman site and m 
using "lipid.itp"
 
#include "ffG43a1.itp"#include "lipid.itp"#include "popc.itp"
#ifdef FLEX_SPC#include "flexspc.itp"#else#include "spc.itp"#endif
#ifdef POSRES_WATER; Position restraint for each water oxygen[ 
position_restraints ];  i funct   fcxfcyfcz   11   
1000   1000   1000#endif
; Include generic topology for ions#include "ions.itp"
[ system ]; NamePure DPPC bilayer with 128 lipids and 3655 water molecules
[ molecules ]; Compound#molsPOPC  128SOL   2460


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