[gmx-users] construct lipid bilayer from a single lipid

[Shanshan Qin]

Yesterday I tried to construct a lipid bilayer through a single lipid. The 
process is like this:
1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0 -o lipid.gro
2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro
3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the 
C value to 0.3
4. editconf -f box.gro -box 3.2 3.2 4.5 -o box1.gro
5. genbox -cp box1.gro -cs -o mix.gro
after these steps ,I got a lipid monolayer and water monolayer got together 
,without water in the lipid hydrophobic tails.However when I ran energy 
minimization steps, it converged to the precision of computer after only 16 
steps and still have very high energy. How can I make the starting 
configuration energy lower?
By the way ,I have tried both steep and cg method, neither worked well.Any 
suggestion will be appreciated.

___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] construct lipid bilayer from a single lipid

[Shanshan Qin]

Hello, gmx-users.Today I tried to construct a lipid bilayer through a single 
lipid. The process is like this:
1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0  -o lipid.gro
2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro
3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the 
C value to 0.3
4. editconf -f box.gro -box 3.2 3.2 4.5 -o box1.gro
5. genbox -cp box1.gro -cs -o mix.gro
after these steps ,I got a lipid monolayer and water monolayer got together 
,without water in the lipid hydrophobic tails.However when I ran energy 
minimization steps, it converged to the precision of computer after only 16 
steps and still have very high energy. How can I make the starting 
configuration energy lower?
By the way ,I have tried both steep and cg method, neither worked well.Any 
suggestion will be appreciated, thanks.___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] construct lipid bilayer from a single lipid

[Shanshan Qin]

 
Hello, gmx-users.Today I tried to construct a lipid bilayer through a single 
lipid. The process is like this:
1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0  -o lipid.gro
2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro
3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the 
C value to 0.3
4. editconf -f box.gro -box 3.2 3.2 4.5 -o box1.gro
5. genbox -cp box1.gro -cs -o mix.gro
after these steps ,I got a lipid monolayer and water monolayer got together 
,without water in the lipid hydrophobic tails.However when I ran energy 
minimization steps, it converged to the precision of computer after only 16 
steps and still have very high energy. How can I make the starting 
configuration energy lower?
By the way ,I have tried both steep and cg method, neither worked well.Any 
suggestion will be appreciated, thanks.___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] construct lipid bilayer from a single lipid

[Shanshan Qin]

Hello, gmx-users.Today I tried to construct a lipid bilayer through a single 
lipid. The process is like this:
1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0  -o lipid.gro
2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro
3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the 
C value to 0.3
4. editconf -f box.gro -box 3.2 3.2 4.5 -o box1.gro
5. genbox -cp box1.gro -cs -o mix.gro
after these steps ,I got a lipid monolayer and water monolayer got together 
,without water in the lipid hydrophobic tails.However when I ran energy 
minimization steps, it converged to the precision of computer after only 16 
steps and still have very high energy. How can I make the starting 
configuration energy lower?
By the way ,I have tried both steep and cg method, neither worked well.Any 
suggestion will be appreciated, thanks.
___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

回复:Re: [Bulk] [gmx-users] a q uestion about potential energy

[taojinwuhan]

 Dear MarkI am very very 
sorry about what I did. I am a green guy so Idon't know the regulations 
and the situations clearly. I will take care and never make such mistakes 
again! Now I have edited my question and posted it again.Thank you 
for your help! Best regards!Paul Tao___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

回复:Re: [Bulk] [gmx-users] a q uestion about potential energy

[taojinwuhan]

 Dear Yany YeThank you for your help. I am indeed a 
new man as you guess. I am very very sorry about what I did and will take 
care to never make such stupid mistakes.The simulation I 
posted is a eq run, and I extracted theprotein potential energy following 
what you taught me before(just want to checkthe protein). What puzzled me 
is that the potential energy in every frame is almost lower than 
-9(you can see it in protein.xvg in attachment),but the average proteinpotential energy in log is just -188 and the RMS-fluctuations is 4146(see 
below). How did gromacs get the avergae value and rms value like these? 
According to my understanding the average energy should also be about 
-9. Does my md run bad?Could you give me a explanation or give me any 
suggestions? Thanks!Best regardsPaul TaoPs: the part of log<==  
###  ==>    <  A V E R A G 
E S  >    <==  ###  
==>   Energies (kJ/mol)   G96Angle    Proper 
Dih.   Improper 
Dih.  
LJ-14        Coulomb-14    
4.47120e+01    2.05332e+01    
1.46051e+01    8.86024e+00    2.87573e+02    LJ 
(SR)         LJ 
(LR) 
Coulomb (SR)  Coul. 
recip.  Potential   
-9.50660e+01   -3.65730e+00   -1.01766e+02   
-3.63918e+02   -1.88123e+02    Kinetic 
En.  Total Energy    Temperature 
Pressure (bar)    6.82162e+01   
-1.19907e+02    6.09296e-01   -1.52389e-01  
Box-X   
 Box-Y  
Box-Z          
   Volume        Density (SI)    3.03565e-02    
3.03565e-02    3.03565e-02    
6.82831e+00    1.49606e-01 
pV   -3.09662e+01   Total Virial 
(kJ/mol)    3.78382e+01    
7.27218e-01   -1.68112e-01    
7.27214e-01    3.77270e+01   -8.52153e-01   -1.68124e-01   -8.52145e-01    
3.91003e+01   Pressure (bar)   
-1.49730e-01   -9.56125e-03    3.1e-03   -9.56121e-03   -1.44637e-01    
5.64105e-03    3.10011e-03    
5.64098e-03   -1.62801e-01   Total Dipole 
(Debye)   -2.13479e+01   -2.18829e+01   
-2.22107e+01    <==  
###  ==>   
 <  R M S - F L U C T U A T I O N S  >    <==  ###  
==>   Energies (kJ/mol)   
G96Angle 
 Proper Dih.  Improper 
Dih.  
LJ-14 Coulomb-14    
9.89738e+02    4.53448e+02    
3.23204e+02    1.94891e+02    6.34017e+03    LJ (SR) 
          LJ (LR)          
   Coulomb (SR)   Coul. 
recip.  Potential    
2.09723e+03    8.06436e+01    
2.24368e+03    8.02594e+03    4.14647e+03  Kinetic 
En.   Total Energy    Temperature    
Pressure (bar)    1.50381e+03    
2.64284e+03    1.34318e+01    3.54340e+00  
Box-X  
Box-Y  
Box-Z Volume   
Density (SI)    6.69374e-01    
6.69374e-01    6.69374e-01    
1.50584e+02    3.29814e+00 
pV    7.19966e+02   Total Virial 
(kJ/mol)    8.49070e+02    
8.20897e+01    7.54720e+01    
8.20897e+01    8.50494e+02    9.04527e+01    7.54718e+01    
9.04529e+01    8.81896e+02   Pressure 
(bar)    3.57605e+00    
8.22075e-01    7.49848e-01    
8.22075e-01    3.55242e+00    8.78451e-01    7.49846e-01    
8.78454e-01    3.95141e+00   Total Dipole 
(Debye)    4.70706e+02    
4.82556e+02    4.89913e+02-  原文  -  
From: mailto:[EMAIL PROTECTED]">Yang 
Ye To: mailto:gmx-users@gromacs.org";>Discussion list for GROMACS users Subject: Re: [Bulk] [gmx-users] a question about potential 
energySent: Sat Aug 11 11:41:35 CST 2007 Hi,  You shall help yourself to find the answer by 
plotting your energy with g_energy.  Have your equilibrated 
your system well? Which stage of simulation are you running with, em, eq 
or production run? Having large fluctuation is sometimes normal and 
sometimes bad.  Also, please attach necessary and concise 
information to the mails. We may open a table-like file (e.g. xvg) for 
energy but not a log file just for energies. I understand that you could 
be new to gromacs, just take note of this.  Regards, 
Yang Ye  On 8/10/2007 3:54 PM, mailto:[EMAIL 
PROTECTED]">[EMAIL PROTECTED] wrote: > > Hi, all 
> > I have found a problem that in my Md run the potential energy 
in every > frame was about -9e+04 while the average potential energy 
of all was > -1.88e+02. What is wrong with it? Why are they so 
different? Can > anybody tell me the reason? Thanks! > 
> pS: the attachement is the md.log. You can clearly see that the > 
average energy is so different with the energy in each frame in it. 
> > Paul > > > > 
 
> 《天龙八部》续作之“仙人指路”8月15日线上热播！ > http://ad1.adpolestar.net/ADPolestar/lgs/way/;er=&mv=710&pu=qiwei&ad=0018235?http://tl.sohu.com/?rcc_id=4bfd05b7d66287271b5738e9be7aae68> > > *用搜狗拼音写邮件，体验更流畅的中文输入>> > http://goto.mail.sohu.com/goto.php3?code=mailadt-ta> >

Re: [gmx-users] Re: question about free energy. Gromacs user

[David Mobley]

Hi,

> I just have a couple of things i want to clarify about the constrain
> distances i used.  The distance I used to pull the ligand and receptor
> apart was a non-bonded distance between the amide nitrogen of the ligand
> and the oxygen carbonyl of the receptor (on both ends).  looking at the
> slowgrowth results of my 5 ns, the distances i specifed increased from
> lambda 0 to 1, however, I didnt get separation as I wanted it since the
> ends just separated and the middle interaction of the ligand-receptor
> stayed intact. nothing unusal happened to the ligand or receptor.
> I dont think my method altered the internal degrees of freedom of the
> ligand. Can you please clarify this issue for me.

In terms of altering the internal degrees of freedom of something, let
me just explain what can go wrong, and you can figure out if it
applies to what you're doing. Basically, suppose you have a ligand
which prefers to be in one conformation when it's bound, and in a
different conformation when it's unbound. Suppose then you apply
constraints, based on the bound structure, to constrain the distance
between atom A in the ligand and reference atom C in the protein, and
to constrain the distance between atom B in the ligand and reference
atom C in the protein. Suppose further that atoms A and B want to be
5A apart when the ligand is in the bound conformation, but 8A when the
ligand is in the unbound conformation. Naturally, looking at the bound
structure, you set your constraints A-C and B-C to pull at the same
rate. Now, the problem occurs if the constraints you've introduced to
the A-C and B-C distances make it hard for the A-B distance to change,
so that when the ligand is pulled out of the protein, distance A-B
remains 5A, though the ligand would prefer to have it be 8A.

The question you have to answer is whether there is any potential that
your constraints would cause this to happen. My hunch is yes: Although
in principle if you constrain A-C and B-C, A-B is not constrained,  in
practice, constraining A-C and B-C probably introduces additional
barriers into the ligand conformational change landscape. I am not
sure though. This is what you have to figure out.

If the constraints do affect the A-B distance in the sense I have
described, then your results will probably be garbage.

David


> I used constraint=all-bonds in my mdp file.
>
> Again, thanks you both for the comments.
>
> Belquis
>
>
>
> >
> >>
> >> Maybe it should be obvious, but (a) why are you constraining two
> >> distances, and (b) are you sure your constraints aren't going to muck
> >> with the internal degrees of freedom for the ligand? I would think one
> >> would like to pull the ligand out of the receptor along some
> >> particular direction, but without doing anything to alter its internal
> >> degrees of freedom, or there would be a free energy associated with
> >> changing its internal degrees of freedom that you wouldn't capture in
> >> the PMF calculation.
> >>
> >
> > I agree with David's comments here.  Check out the 'Special Topic'
> > section
> > of the GMX manual.   you can either do a pulling simulation or umbrella
> > sampling (where the position and constrain the ligand on some rxn
> > coordinate, in several simulation).  The output of such simulatsions is a
> > *.pdo file, which you can then run g_wham on to obtain a PMF.
> > ___
> > 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]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
>
>
> ___
> 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]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: doing simplest simulations

[Nicolas Schmidt]

>> Second: Am I simulating fixed connections? 

>No

I once wrote in a mail in may I think:

>> This may be a really simple question, I know, but still...
>>
>> How can I set up a fixed connection between two atoms of a molecule? When I 
>> choose the 5th bondtype in my topology-file I get the following output from 
>> grompp (though it's processing, so I CAN start mdrun afterwards):
>>
>> WARNING 1 [file "ethane.itp", line 12]:
>>   No default Connect Bonds types, using zeros
>>
>> Either way I'm not sure how the distance of these two atoms is processed, so 
>> there is NO parameter that is specifying this bond-type (and a constraint 
>> would be processed by gromacs, wouldn't it? And I don't want it to, cause I 
>> want the simulation to be as simple as possible)
>>
>> By the way, I wanna simulate a huge system of ethane and take a look at the 
>> processing time per simulated step, is there an output-file thats reading 
>> this?
>>
>> Thanks in advance to everyone who is replying, it's so hard when you're 
>> stuck. 
>[ constraint ]
>; i j type length
>1 2 1 0.15
>
>-- 
>David. 

So what's my mistake? I posted my .itp-file, do I have to do a change in the 
forcefield-files? When 'yes', what change? ;-)

>> Are my chosen options on the .mdp-file therefor correct? 
>By comparison with what?

To build up a fixed connection. What therefor to choose in the bonds section of 
the .mdp-file? constraints = none, all??? 

Is in the Electrostatics-section of the .mdp-file
>coulombtype = cut-off
>rcoulomb = 0
sufficient to not simulate any electrostatics?

If not, what else should I do? ;-)

to Mark:

thanks for your help, it's definitely not in the way that I'm refusing to take 
your advice 'bout the tutorials, but it's sometimes uneasy to find out some 
kind of an exception from the rule (fixed connections, no electrostatics, 
prefering speed to accuracy, and so on). Why doing an energy minimization when 
I equilibrate at an higher temperature and cool down afterwards? And of course 
I'm a newbie, otherwise I'd answer questions and not ask them. 

and most of all, I just have to do ONE set of simulations (with an various 
amount of molecules) to compare gromacs' speed in simulating large systems of 
simple gas molecules. I wanna do well, otherwise I'd just take what I got from 
the already finished simulations. But afterwards I'm done and won't bother you 
again. ;-) 

Thanks again.

Nicolas

posted the most recent .mdp-file and .itp-file as well.




-- 
GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS.
Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail


md.mdp
Description: application/mdp


OneEthane.itp
Description: Binary data
___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] a basic question

[Q733]

Mark,thanks very much. I will follow your suggestion and check wiki.gromacs.org.___
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]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php