Re: [gmx-users] simulation of protein in popc box

[Pawan Kumar]

Hello Shamik,

Going through the membrane protein tutorial will help you to get answers to
these questions.
The lipid.itp file has to be modified and edited depending on the force
fields being used like opls force field or the gromos96 force field.
Popc.itp file should also be included in order to include the topology for
the POP residues. lipid.itp file is used to include more of interaction
parameters.

Regards,
Pawan

On Fri, May 22, 2009 at 4:58 PM, Samik Bhattacharya
wrote:

> Thanks pawan, for helping but one problem still remains that is how to
> incorporate the .itp file inside the topology file and which .itp file
> should i include is it the lipid.itp orr POPC.itp??
> thanx for your help
> Shamik
>
>
>
>
>
> Greetings from Pawan.
> Topologies for lipids like POP are not available in the topology database
> in gromacs.
> So the starting point would be to generate a topology and a gro file for
> the protein alone as such and then edit the topology to include the .itp
> files as specifically needed for the lipids.
>
> Regards,
> Pawan
>
> On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya 
> http://mc/compose?to=samikb...@yahoo.co.in>
> > wrote:
>
>>  hi
>> i am new to Gromacs. i want to simulate a protein inside a lipid
>> box(preferably POPC or POPE). i have generated the protein inside the POPC
>> box complex. But whenever i am going to build the .gro and .top file of that
>> complex with pdb2gmx an error is creeping in saying "Cant find POP in
>> residue topology database". it cant recognise the lipid.itp and popc.itp
>> files which i've already put into the top directory.
>> plese help me out.
>> thank you
>>
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Re: [gmx-users] simulation of protein in popc box

[Pawan Kumar]

Hello,

Greetings from Pawan.
Topologies for lipids like POP are not available in the topology database in
gromacs.
So the starting point would be to generate a topology and a gro file for the
protein alone as such and then edit the topology to include the .itp files
as specifically needed for the lipids.

Regards,
Pawan

On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya
wrote:

> hi
> i am new to Gromacs. i want to simulate a protein inside a lipid
> box(preferably POPC or POPE). i have generated the protein inside the POPC
> box complex. But whenever i am going to build the .gro and .top file of that
> complex with pdb2gmx an error is creeping in saying "Cant find POP in
> residue topology database". it cant recognise the lipid.itp and popc.itp
> files which i've already put into the top directory.
> plese help me out.
> thank you
>
> --
> Explore and discover exciting holidays and getaways with Yahoo! India
> Travel Click 
> here!
>
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Re: [gmx-users] problem with system neutralization

[Pawan Kumar]

Hello,

Greetings from Pawan.
Giving the command and the options being used will be much better to give
any further probable suggestions.
Just using " -np 4 " wont solve the problem as such. You should specify the
" -pname " option also. You can use NA+ ions to neutralize the system as its
having negative charge. And when specifying the -np or -nn option u need not
use -neural option.

Regards,
Pawan



On Fri, May 22, 2009 at 4:30 PM, Stefano Meliga  wrote:

> Thanks Pawan,
>
> I added 4 positive ions as you suggested but the system total charge
> reported in genion.log is still -4!
>
> Why?
>
> Cheers,
>
> Stefano
>
>
> Pawan Kumar ha scritto:
>
>> Hello,
>>
>> Greetings from Pawan.
>> -np is a parameter used to add the nmber of positive ions.
>> when u have -4 negative charge u should give -np 4.
>> -np with -pname will be more appropriate.
>> see through this website for the proper usage of genion options.
>> http://www.gromacs.org/documentation/reference_3.3/online/genion.html
>>
>> Regards,
>> Pawan
>> On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga > smel...@gmail.com>> wrote:
>>
>>Dear all,
>>
>>As the on-screen output of grompp says, my system has non-zero
>>total charge = -4.000
>>
>>Thus, I'm trying to neutralize the system using genion with this
>>command line:
>>
>>genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>>4AKEallHsol_pre.top -neutral
>>
>>The problem is that the on-screen output says:
>>
>>"No ions to add and no potential to calculate"
>>as the system was already neutral, I guess.
>>
>>I then tryied with the command line:
>>
>>genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>>4AKEallHsol_pre.top -neutral -np 50 -g
>>
>>Ions are added to the SOL group but the total charge remains -4,
>>as the log file says.
>>
>>Do you know the reason?
>>
>>Thanks a lot,
>>
>>Stefano
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Re: [gmx-users] problem with system neutralization

[Pawan Kumar]

Hello,

Greetings from Pawan.
-np is a parameter used to add the nmber of positive ions.
when u have -4 negative charge u should give -np 4.
-np with -pname will be more appropriate.
see through this website for the proper usage of genion options.
http://www.gromacs.org/documentation/reference_3.3/online/genion.html

Regards,
Pawan
On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga  wrote:

> Dear all,
>
> As the on-screen output of grompp says, my system has non-zero total charge
> = -4.000
>
> Thus, I'm trying to neutralize the system using genion with this command
> line:
>
> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top
> -neutral
>
> The problem is that the on-screen output says:
>
> "No ions to add and no potential to calculate"
> as the system was already neutral, I guess.
>
> I then tryied with the command line:
>
> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top
> -neutral -np 50 -g
>
> Ions are added to the SOL group but the total charge remains -4, as the log
> file says.
>
> Do you know the reason?
>
> Thanks a lot,
>
> Stefano
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Re: [gmx-users] How to remove water from lipid bilayer core

[Pawan Kumar]

Hello Anirban,

Greetings from Pawan.
You can find the scripts in this webiste :
http://wiki.gromacs.org/index.php/Membrane_Simulations

Regards,
Pawan

On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh wrote:

> Hi ALL,
>
> I have a built a system of protein embeded in lipid bilayer and solvated it
> according to the GROMACS membrane simulation tutorial. I want to delete a
> few water molecules that are there in the hydrophobic core of the bilayer. I
> deleted them manually from the .gro file and corrected the atom numbers, but
> still getting an error:
> -
> Invalid line in prt_genbox_MOD.gro for atom 73510:
>   10.81119  10.81119  10.01306
> -
>
> How can I modify the last line and get a correct .gro file by removing the
> unwanted waters? In the tutorial it is stated that there are some scripts to
> remove the unwanted waters. Can anyone provide me such a script.
> Any suggestion is welcome.
>
>
>
> Regards,
>
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
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Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

[Pawan Kumar]

Hello Anirban,

This is due to some wrong editing and modifications of the .itp files.
Please follow the tutorial carefully. The explanation for each modification
is also given quite clearly.

Regards,
Pawan

On Tue, May 12, 2009 at 2:26 PM, Anirban Ghosh wrote:

> Hello Pawan and Justin,
>
> Thanks for the reply.
> I have removed the HW entries from the ffG53a6nb_lipid.itp file and still
> getting the error:
>
> --
> Fatal error:
> Unknown atomtype OW
>
> --
>
> Pawan can you just send me your modified ffG53a6nb_lipid.itp file.
> Please suggest.
>
> Regards,
>
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
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Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

[Pawan Kumar]

Hi Anirban,

I have also followed Justin sir's tutorial.
You should not remove the OW entries.
You can remove the HW entries for sure and then this will work.

Regards,
Pawan

On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh wrote:

> Hello Justin,
>
> Thanks a lot for the reply. Your tutorial is indeed very good.
> I followed your tutorial on protein-lipid simulation. I added the
> non-bonded parameters from the lipid.itp file to the ffG53a6nb_lipid.itp
> file. You have told to either delete the atom-type HW entries having zero
> values in the non-bonded section or replace them with H. But the HW values
> are not zero. And they are also present in the "pairlist" section. So should
> I change in this section also? And when I am running the grompp command I am
> getting the error "Atom-type OW not found". So should I also delete the OW
> entries or should I replace them? If replace, then with what? Should I
> replace all the OW and HW entries throughout the ffG53a6nb_lipid.itp file?
> Please advice.
>
> Regards,
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
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Re: [gmx-users] protein falls apart in energy minimization

[Pawan Kumar]

hi,

Defining a specific box size with -d option in editconf will help to
overcome this problem...

Regards,
Pawan

On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng  wrote:

> hi all
>
> I am running Gromacs on a protein consisted of three chains. But no matter
> how I tried, the protein always falls into three parts (corresponding to
> each chain) after a simple 2000 steps energy minimization. Can anyone help
> me please? Thanks.
>
> Zhong Zheng
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Re: [gmx-users] Warning: Pressure scaling more than 1%.

[Pawan Kumar]

Hi,

Increasing the tau-p value in the parameter file should help.

Regards,
Pawan

On Mon, May 11, 2009 at 11:06 AM, Zhanglin Ni  wrote:

> Dear all,
> when I run position-restrained simulation (total 15000steps). when it
> reached 740 steps
> Step 741  Warning: Pressure scaling more than 1%.
>
> Step 742  Warning: Pressure scaling more than 1%.
>
> Step 743  Warning: Pressure scaling more than 1%.
>
> Step 744  Warning: Pressure scaling more than 1%.
>
> Step 745  Warning: Pressure scaling more than 1%.
>
> Step 746  Warning: Pressure scaling more than 1%.
>
> Step 747  Warning: Pressure scaling more than 1%.
>
> Step 748  Warning: Pressure scaling more than 1%.
>
> I knew the error was shown in the Gromacs websites. But after I read those,
> I still donot know how to solve it. any one give some clue. Thanks
> Johnny
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Re: [gmx-users] problem with genion

[Pawan Kumar]

Use solvent group (Group 13) for neutralization.

Pawan

On Sat, May 9, 2009 at 5:03 PM, nitu sharma  wrote:

> Dear all,
>
>Thanks for solving lot of problem of me in doing
> membrane membrane protein simulation. Now I have a one problem I want to add
> ion to the my system by genion command
>
> for this i am following justin's tutorial  but in the genion step when i
> have put the command like this -
>  genion -s ions.tpr -o compsol-ions.gro -p topol1.top -pname NA+ -nname CL-
> -np 1
>   and I choose the 0 for adding ions to the system then I have  got the
> error like this -
>
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Group 0 (  System) has 598751 elements
> Group 1 ( Protein) has  9902 elements
> Group 2 (   Protein-H) has  7778 elements
> Group 3 ( C-alpha) has  1000 elements
> Group 4 (Backbone) has  3000 elements
> Group 5 (   MainChain) has  4000 elements
> Group 6 (MainChain+Cb) has  4922 elements
> Group 7 ( MainChain+H) has  4961 elements
> Group 8 (   SideChain) has  4941 elements
> Group 9 ( SideChain-H) has  3778 elements
> Group10 ( Prot-Masses) has  9902 elements
> Group11 ( Non-Protein) has 588849 elements
> Group12 (DMPC) has  5520 elements
> Group13 ( SOL) has 583329 elements
> Group14 (   Other) has 588849 elements
> Select a group: 0
> Selected 0: 'System'
>
> ---
> Program genion, VERSION 4.0.3
> Source code file: gmx_genion.c, line: 443
>
> Fatal error:
> Your solvent group size (598751) is not a multiple of 8
> ---
>
> can any suggest me what should I do to solve this problem . I am doing
> first time all these these things so if anyone can suggest me something I
> will be really thankful for him/her.
>
> Thanks a lot.
>
> Nitu Sharma
> School of life sciences
> Jawaherlal nehru university
> New delhi, india
>
>
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Re: [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

[Pawan Kumar]

hi,

It will be better to check the energy after the final production run 

Pawan

On Fri, May 1, 2009 at 12:15 AM, Halie Shah  wrote:

>
> Hi!
>
> I have just completed a position restrained dynamics run on my protein with
> GROMACS 3.3.3 and I generated an xvg file with the g_energy command...I
> noticed in this that the energy for time step 0 was 0.88 (near 0) kj
> mol/S-1/N while the energy for time step 0.2ps was 1158after this the
> rest of the time steps (up to 20ps) were roughly around 1150. I'm wondering
> why the energy at the start is so low for my protein (which I energy
> minimized)...I assumed it would be near 1150. Is this a problem/what does it
> mean? Os it fine to move on and do an mdrun?
>
> Thanks so much,
> Halie Shah
> University of Houston
> Briggs Computational Biology Lab
>
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Re: [gmx-users] mdrun error

[Pawan Kumar]

probably a bad starting structure...
check this website for  pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors

regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora wrote:

> I am trying to run the simulation of protein ligand complex.
> But after running the mdrun by giving command-"grompp –f md.
> mdp –c pr.gro –p trp.top –o md.tpr "
> and then "nohup mdrun –deffnm md & "
> the md.log file is showing the following message-
> Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
> 1.01684
>
> Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
> 0.947161
>
> Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
> 1.01207
>
> Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
> 1.18248
>
> Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
> 0.867467
>
> Step 16, time 0.032 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.099556 (between atoms 1396 and 1398) rms 0.028595
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 23   30.80.1740   0.1569  0.1470
>  38 40   32.00.1740   0.1583  0.1470
>  54 56   33.00.1740   0.1588  0.1470
>  56 57   30.60.1810   0.1623  0.1530
>  67 69   31.40.1740   0.1568  0.1470
> 104106   32.60.1740   0.1588  0.1470
> 106107   31.10.1811   0.1632  0.1530
> 216218   31.80.1741   0.1584  0.1470
> I am attaching my md.mdp file.Please help me in this regard.
>
> --
> Sheetal Arora
> M.Tech(Biotechnology & Medical Engg)
>
> NIT Rourkela
>
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Re: [gmx-users] problem in energy minimisation

[Pawan Kumar]

On Fri, Apr 24, 2009 at 4:13 PM, nitu sharma  wrote:

> Dear Mark
>
> After doing second step of inflategro  i.e compression step  when I
> did the enery minimisation  with nstep-1 in parameter file  it
> terminated after 1547 steps and written that -
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 1547 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  =  6.2109662e+05
> Maximum force =  2.1254887e+04 on atom 6781
> Norm of force =  7.1093488e+02
>
> Can u suggest me probable solution of this problem .I am unable to
> understand why this problem comes?


its because of clashes between the protein and the lipid molecules.


>
>
> Thanks a lot
> Nitu Sharma
> Structural biology lab
> School of life Sciences
> Jawaherlal Nehru University
>
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Re: [gmx-users] Membrane protein tutorial

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
It has worked now.
I dint edit the index file before also. The problem was with the .mdp file.
It was recognising lipids as POP and I gave as POPC in the .mdp file. Now
there are no more errors.
Thanks a lot.

Thanking you,
Pawan

On Thu, Apr 9, 2009 at 3:35 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Hello Sir,
>>
>> The whole point in making an index file was to merge the sol and cl- ions.
>> If i put popc also in the index file then it wont make any much useful
>> group because lipids needs to be defined in a different group as I have read
>> in various archives. Please do correct me if I am wrong.
>>
>>
> What you need is a POPC_CL- group in addition to the other standard groups.
> There is a page in my tutorial (which you referenced earlier) that describes
> exactly how to do this:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
>
> So your index file should contain System, all the relevant protein groups,
> POPC, SOL, CL-, and SOL_CL-.  If you are considering manually modifying this
> file in some way (as I am guessing you have), don't.
>
> -Justin
>
>  Thanking you,
>> Pawan
>>
>>
>>
>> On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren <
>> dallas.war...@pharm.monash.edu.au > dallas.war...@pharm.monash.edu.au>> wrote:
>>
>>Well, as the error says, popc isn't defined in the index file.Seems
>> grompp is looking for a popc entry in the index file, and
>>can't find it.  So, I would hazard to say, you need to define it.
>>Catch ya,
>>
>>Dr. Dallas Warren
>>Department of Pharmaceutical Biology and Pharmacology
>>Pharmacy and Pharmaceutical Sciences, Monash University
>>381 Royal Parade, Parkville VIC 3010
>>dallas.war...@pharm.monash.edu.au
>><mailto:dallas.war...@pharm.monash.edu.au>
>>+61 3 9903 9167
>>-
>>When the only tool you own is a hammer, every problem begins to
>>resemble a nail.
>>
>>
>>  --------
>>*From:* gmx-users-boun...@gromacs.org
>><mailto:gmx-users-boun...@gromacs.org>
>>[mailto:gmx-users-boun...@gromacs.org
>><mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *Pawan Kumar
>>*Sent:* Thursday, 9 April 2009 2:39 PM
>>*To:* jalem...@vt.edu <mailto:jalem...@vt.edu>; Discussion list
>>
>>for GROMACS users
>>*Subject:* Re: [gmx-users] Membrane protein tutorial
>>
>>Hello sir,
>>
>>Thanks for such a explanatory tutorial.
>>I am stuck with one error now.
>>I have protein, popc, sol and cl- in my system.
>>I have merged the sol and cl- using make_ndx.
>>But when I run grompp I get the error like this "popc not
>>defined in the index file".
>>The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top
>>-o box_pr.tpr
>>Any suggestions please.
>>*
>>pr.mdp file :*
>>title   =  protein in popc bilayer
>>cpp =  /usr/bin/cpp
>>define  =  -DPOSRES -DPOSRES_LIPID
>>constraints =  all-bonds
>>constraint-algorithm=  Lincs
>>integrator  =  md
>>dt  =  0.002  nsteps  =  5000
>>nstcomm =  1
>>nstxout =  50
>>nstvout =  1000
>>nstfout =  0
>>nstlog  =  10
>>nstenergy   =  10
>>nstlist =  10
>>ns_type =  grid
>>rlist   =  1
>>coulombtype =  PME
>>rcoulomb=  1
>>vdw-type=  Cut-off
>>rvdw=  1
>>; Berendsen temperature coupling is on in two groups
>>tcoupl  = berendsen
>>tc_grps = Protein POPC SOL_CL-
>>tau_t   = 0.1 0.1 0.1
>>ref_t   = 300 300 300
>>; Energy monitoring
>>energygrps=  Protein POPC SOL_CL-
>>; Pressure coupling is on
>>;Pcoupl  =  berendsen
>>tau_p   =  2.0 2.0
>>compressibility

Re: [gmx-users] Re: Membrane protein tutoria

[Pawan Kumar]

Thanks for your mail sir.
I will do some reading as per your suggestion.

On Thu, Apr 9, 2009 at 10:45 AM,  wrote:

> Dear Pawan,
>
> I suggest that you try doing some protein in water simulations or some
> available tutorials before you proceed with your bilayer study. You might
> also consider reading the error messages more carefully and attempting to
> troubleshoot based on these messages. If the error message is "popc not
> defined in the index file" or "Atom 1 defined in multiple groups (1 & 3)"
> then I think that you already have the information that you need. At least
> in the second case you have at least as much information as we do -- one
> might ask why you can't have an atom in multiple groups, and I'll hint that
> this is not an .ndx file problem in and of itself.
>
> I hope that this comes across as I intend since I'm only trying to be
> helpful to you here. Bilayer simulations are not nearly as simple as those
> with proteins in water and if you don't understand the role of the .ndx file
> then your time might be better spent reading the manual and running some
> simpler simulations. Why do I say this? Mostly because there is no error
> given for "your bilayer has entered the gel phase" or "your temperature
> coupling of a group with too few atoms has lead to incorrect results" and it
> is thus useful to be clear what is going on before you decide what to do
> since you can still do things incorrectly without getting an error message.
>
> Further, I would prefer if you pick some more useful subject lines. This
> has nothing to do with the membrane protein tutorial that Justin recently
> provided. At least there is no more "doubt about membrane simulation" ;)
>
> Chris.
>
>
>
> -- original message --
>
> Hello Mark Sir,
>
> I have tried that way also.
> The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
> topol.top -o box_pr.tpr
> But this time i get an error like this "Atom 1 defined in multiple groups
> (1
> & 3). "
> How to overcome this error ?
>
> Thanking you,
> Pawan
>
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Re: [gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello sir,

Thanks for your reply.
I have used this .mdp file. Is there anything wrong in the mdp file which I
am using ?
To tell you in detail : First I have done energy minimization. Output of
this step (box_em.pdb) is used to create an index group for sol and cl- ions
using make_ndx. Then I am trying to run grompp using this particular .mdp
file before position restraint mdrun.

*pr.mdp file :*
title   =  protein in popc bilayer
cpp =  /usr/bin/cpp
define  =  -DPOSRES -DPOSRES_LIPID
constraints =  all-bonds
constraint-algorithm=  Lincs
integrator  =  md
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
vdw-type=  Cut-off
rvdw=  1
; Berendsen temperature coupling is on in two groups
tcoupl  = berendsen
tc_grps = Protein POPC SOL_CL-
tau_t   = 0.1 0.1 0.1
ref_t   = 300 300 300
; Energy monitoring
energygrps=  Protein POPC SOL_CL-
; Pressure coupling is on
Pcoupl  =  berendsen
tau_p   =  2.0 2.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

Thanking you,
Pawan

On Thu, Apr 9, 2009 at 10:38 AM, Mark Abraham wrote:

> Pawan Kumar wrote:
>
>> Hello Mark Sir,
>>
>> I have tried that way also.
>> The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
>> topol.top -o box_pr.tpr
>> But this time i get an error like this "Atom 1 defined in multiple groups
>> (1 & 3). "
>> How to overcome this error ?
>>
>
> You can't have the same atom in multiple groups used for the same purpose
> within mdrun (e.g. T-coupling or energy). I guess you've constructed your
> index file in a manner that is inconsistent with your use of it.
>
>
> Mark
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Re: [gmx-users] pdb file and force filed

[Pawan Kumar]

Hello,

For usual peptides having amino acids you need not use Dundee Prodrg server.
pdb2gmx itself will generate the required .itp and .gro files.
If u were using opls force fiels in tinker then use the same force fields in
gromacs also because atom types are defined in different ways in different
force fields.
May be this explanation will help.

Regards,
Pawan

On Thu, Apr 9, 2009 at 10:17 AM, Bhawana Gupta
wrote:

> Hello sir,
>
> From last few days , i was using TINKER for implicit simulations using
> force field oplsaa
> Now for explicit one, i switched to gromacs version 4.0.But if i take pdb
> file from tinker (molecular modelling software) and paste it in The Dundee
> Prodrg server. i got my *.itp file, *.gro file.
>
> But if i use force field as ffoplsaa or ffG43a1 or any other force field
> except ffgmx. I always got error in atom type not found.
>
> Tell me what to do.
>
> Can i switch to gromacs older version i.e.3.3.1???
>
> Whether i can use The Dundee Prodrg server for peptides having usual amino
> acid???
>
> With regards,
> Bhawana
>
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Re: [gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello Sir,

The whole point in making an index file was to merge the sol and cl- ions.
If i put popc also in the index file then it wont make any much useful group
because lipids needs to be defined in a different group as I have read in
various archives. Please do correct me if I am wrong.

Thanking you,
Pawan



On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren <
dallas.war...@pharm.monash.edu.au> wrote:

>  Well, as the error says, popc isn't defined in the index file.  Seems
> grompp is looking for a popc entry in the index file, and can't find it.
> So, I would hazard to say, you need to define it.
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology and Pharmacology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>  --
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Pawan Kumar
> *Sent:* Thursday, 9 April 2009 2:39 PM
> *To:* jalem...@vt.edu; Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Membrane protein tutorial
>
> Hello sir,
>
> Thanks for such a explanatory tutorial.
> I am stuck with one error now.
> I have protein, popc, sol and cl- in my system.
> I have merged the sol and cl- using make_ndx.
> But when I run grompp I get the error like this "popc not defined in the
> index file".
> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
> box_pr.tpr
> Any suggestions please.
> *
> pr.mdp file :*
> title   =  protein in popc bilayer
> cpp =  /usr/bin/cpp
> define  =  -DPOSRES -DPOSRES_LIPID
> constraints =  all-bonds
> constraint-algorithm=  Lincs
> integrator  =  md
> dt  =  0.002
> nsteps  =  5000
> nstcomm =  1
> nstxout =  50
> nstvout =  1000
> nstfout =  0
> nstlog  =  10
> nstenergy   =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1
> coulombtype =  PME
> rcoulomb=  1
> vdw-type=  Cut-off
> rvdw=  1
> ; Berendsen temperature coupling is on in two groups
> tcoupl  = berendsen
> tc_grps = Protein POPC SOL_CL-
> tau_t   = 0.1 0.1 0.1
> ref_t   = 300 300 300
> ; Energy monitoring
> energygrps=  Protein POPC SOL_CL-
> ; Pressure coupling is on
> ;Pcoupl  =  berendsen
> tau_p   =  2.0 2.0
> compressibility =  4.5e-5 4.5e-5
> ref_p   =  1.0 1.0
> Pcoupl_type =  semiisotropic
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp=  300.0
> gen_seed=  173529
>
> Thanking you,
> Pawan
>
>
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Re: [gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello Mark Sir,

I have tried that way also.
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
topol.top -o box_pr.tpr
But this time i get an error like this "Atom 1 defined in multiple groups (1
& 3). "
How to overcome this error ?

Thanking you,
Pawan

On Thu, Apr 9, 2009 at 10:14 AM, Mark Abraham wrote:

> Pawan Kumar wrote:
>
>> Hello sir,
>>
>> Thanks for such a explanatory tutorial.
>> I am stuck with one error now.
>> I have protein, popc, sol and cl- in my system.
>> I have merged the sol and cl- using make_ndx.
>> But when I run grompp I get the error like this "popc not defined in the
>> index file".
>> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
>> box_pr.tpr
>>
>
> As I said last time, you'll need to give grompp the index file so that it
> can make sense of your use of the new group(s) name(s).
>
> Mark
>
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Re: [gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello sir,

Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this "popc not defined in the
index file".
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
box_pr.tpr
Any suggestions please.
*
pr.mdp file :*
title   =  protein in popc bilayer
cpp =  /usr/bin/cpp
define  =  -DPOSRES -DPOSRES_LIPID
constraints =  all-bonds
constraint-algorithm=  Lincs
integrator  =  md
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
vdw-type=  Cut-off
rvdw=  1
; Berendsen temperature coupling is on in two groups
tcoupl  = berendsen
tc_grps = Protein POPC SOL_CL-
tau_t   = 0.1 0.1 0.1
ref_t   = 300 300 300
; Energy monitoring
energygrps=  Protein POPC SOL_CL-
; Pressure coupling is on
;Pcoupl  =  berendsen
tau_p   =  2.0 2.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

Thanking you,
Pawan
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Thanks for your mail.
I will work on this.

Thanking you,
Pawan


On 4/7/09, Mark Abraham  wrote:
>
> Pawan Kumar wrote:
>
>> Hello Sir,
>>
>> Can you please tell me how to couple ions with SOL ?
>> Is there any command in gromacs to do that ?
>>
>
> You need to define a group with SOL and the ions in an index file. This is
> uses as input to grompp so that it can make sense of the same group name
> when used in the .mdp file. See
> http://wiki.gromacs.org/index.php/Index_File
>
> Mark
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hello Sir,

Can you please tell me how to couple ions with SOL ?
Is there any command in gromacs to do that ?

Thanking you,
Pawan

On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham wrote:

> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Sorry for the inconvenience about the .mdp file.
>> The mdp file used for the final run is
>> *_
>> final.mdp file_*_
>>
>> _title   =  Protein in POPC bilayer
>> cpp =  /usr/bin/cpp
>> constraints =  all-bonds
>> constraint-algorithm=  Lincs
>> integrator  =  md
>> dt  =  0.002   nsteps  =  5000   nstcomm
>>   =  1
>> nstxout =  50
>> nstvout =  1000
>> nstfout =  0
>> nstlog  =  10
>> nstenergy   =  10
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1
>> coulombtype =  PME
>> rcoulomb=  1
>> vdw-type=  Cut-off
>> rvdw=  1
>> ; Berendsen temperature coupling is on in two groups
>> tcoupl  = berendsen
>> tc_grps = Protein POPC SOL CL-
>> tau_t   = 0.1 0.1 0.1 0.1
>> ref_t   = 300 300 300 300
>>
>
> Don't couple ions seperately. See
> http://wiki.gromacs.org/index.php/Thermostats
>
> Mark
>
>  ; Energy monitoring
>> energygrps=  Protein POPC SOL CL-
>> ; Pressure coupling is on
>> ;Pcoupl  =  berendsen
>> tau_p   =  2.0 2.0
>> compressibility =  4.5e-5 4.5e-5
>> ref_p   =  1.0 1.0
>> Pcoupl_type =  semiisotropic
>> ; Generate velocites is on at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  173529
>> _*
>> mdp file for position restraint mdrun*_
>>
>> title   =  Protein in POPC bilayer
>> cpp =  /usr/bin/cpp
>> define  =  -DPOSRES -DPOSRES_LIPID
>> constraints =  all-bonds
>> constraint-algorithm=  Lincs
>> integrator  =  md
>> dt  =  0.002   nsteps  =  5000   nstcomm
>>   =  1
>> nstxout =  50
>> nstvout =  1000
>> nstfout =  0
>> nstlog  =  10
>> nstenergy   =  10
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1
>> coulombtype =  PME
>> rcoulomb=  1
>> vdw-type=  Cut-off
>> rvdw=  1
>> ; Berendsen temperature coupling is on in two groups
>> tcoupl  = berendsen
>> tc_grps = Protein POPC SOL CL-
>> tau_t   = 0.1 0.1 0.1 0.1
>> ref_t   = 300 300 300 300
>> ; Energy monitoring
>> energygrps=  Protein POPC SOL CL-
>> ; Pressure coupling is on
>> ;Pcoupl  =  berendsen
>> tau_p   =  2.0 2.0
>> compressibility =  4.5e-5 4.5e-5
>> ref_p   =  1.0 1.0
>> Pcoupl_type =  semiisotropic
>> ; Generate velocites is on at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  173529
>>
>>
>> Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Pawan Kumar wrote:
>>
>>
>>Respected Sir,
>>
>>Greetings from Pawan.
>>   1. Were there gaps between the water and lipid
>> headgroups?
>> If so,
>>   the lipids may be pulling towards the solvent.  Restrain the
>>lipids
>>   and run an equilibration for a longer time.
>>
>>Gap was there when  I used a  value of 0.5 in the vdwradii.dat
>>file. The gap reduced as I decreased the value from 0.5 to 0.35
>>to the default of 0.15. I tried all the three possibilities.
>>When I used the default vdwradii.dat file and made the solvation
>>followed by simulation runs the lipids didnt pull apart. But
>>there were water molecules on the sides of the bilayer and not
>>in the interior.
>>
>>
>>This indicates to me that the gaps are causing the problem.  Do not
>>run simulations with water in or around the lipids; it is not
>>realistic.  You can

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Sorry for the inconvenience about the .mdp file.
The mdp file used for the final run is
*
final.mdp file**

*title   =  Protein in POPC bilayer
cpp =  /usr/bin/cpp
constraints =  all-bonds
constraint-algorithm=  Lincs
integrator  =  md
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
vdw-type=  Cut-off
rvdw=  1
; Berendsen temperature coupling is on in two groups
tcoupl  = berendsen
tc_grps = Protein POPC SOL CL-
tau_t   = 0.1 0.1 0.1 0.1
ref_t   = 300 300 300 300
; Energy monitoring
energygrps=  Protein POPC SOL CL-
; Pressure coupling is on
;Pcoupl  =  berendsen
tau_p   =  2.0 2.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
*
mdp file for position restraint mdrun*

title   =  Protein in POPC bilayer
cpp =  /usr/bin/cpp
define  =  -DPOSRES -DPOSRES_LIPID
constraints =  all-bonds
constraint-algorithm=  Lincs
integrator  =  md
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
vdw-type=  Cut-off
rvdw=  1
; Berendsen temperature coupling is on in two groups
tcoupl  = berendsen
tc_grps = Protein POPC SOL CL-
tau_t   = 0.1 0.1 0.1 0.1
ref_t   = 300 300 300 300
; Energy monitoring
energygrps=  Protein POPC SOL CL-
; Pressure coupling is on
;Pcoupl  =  berendsen
tau_p   =  2.0 2.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


Thanking you,

Yours sincerely,
Pawan

On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>>
>> Respected Sir,
>>
>> Greetings from Pawan.
>>
>>1. Were there gaps between the water and lipid headgroups?  If so,
>>the lipids may be pulling towards the solvent.  Restrain the lipids
>>and run an equilibration for a longer time.
>>
>> Gap was there when  I used a  value of 0.5 in the vdwradii.dat file. The
>> gap reduced as I decreased the value from 0.5 to 0.35 to the default of
>> 0.15. I tried all the three possibilities.
>> When I used the default vdwradii.dat file and made the solvation followed
>> by simulation runs the lipids didnt pull apart. But there were water
>> molecules on the sides of the bilayer and not in the interior.
>>
>>
>
> This indicates to me that the gaps are causing the problem.  Do not run
> simulations with water in or around the lipids; it is not realistic.  You
> can clean up such a starting structure, either by some clever script like
> those on the wiki, or by looking at the structure, taking note of which
> water molecules are offending, and deleting them manually from the
> coordinate file.
>
> The other option is to temporarily give genbox a box that is slightly
> smaller in the x-y dimensions, so that it will try to place less water
> around the POPC periphery.
>
>
>>2. 5000 steps is far too short to expect any realistic behavior for
>>lipids. Equilibration can take upwards of 10-20 ns.
>>
>> As per your suggestion I have made the final mdrun now again with 50
>> steps. Hopefully this will work.
>>
>>
>>3. You haven't mentioned the contents of your .mdp file.  Maybe
>>you're doing something wrong.
>>
>> I am using the same .mdp file which I posted before. I have just removed
>> the restraints.
>>
>>
> I don't have record of the previous email; as a general guide, post the
> .mdp by default when experiencing weird behavior.  That way the users on
> this list won't have to go combing through the archive to find it.  If you
> want free help, make it easy to help you :)
>
> -Justin
>
>
>>4. Are you using Gromos/Berger o

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.


> 1. Were there gaps between the water and lipid headgroups?  If so, the
> lipids may be pulling towards the solvent.  Restrain the lipids and run an
> equilibration for a longer time.

Gap was there when  I used a  value of 0.5 in the vdwradii.dat file. The gap
reduced as I decreased the value from 0.5 to 0.35 to the default of 0.15. I
tried all the three possibilities.
When I used the default vdwradii.dat file and made the solvation followed by
simulation runs the lipids didnt pull apart. But there were water molecules
on the sides of the bilayer and not in the interior.


> 2. 5000 steps is far too short to expect any realistic behavior for lipids.
> Equilibration can take upwards of 10-20 ns.

As per your suggestion I have made the final mdrun now again with 50
steps. Hopefully this will work.

>
> 3. You haven't mentioned the contents of your .mdp file.  Maybe you're
> doing something wrong.

I am using the same .mdp file which I posted before. I have just removed the
restraints.

>
> 4. Are you using Gromos/Berger or OPLS/converted Berger for your system?
>  There have been so many of these questions from different users over the
> last few days that it's hard to keep track.  If you are using OPLS/converted
> Berger you may have made a mistake in translating the C6/C12 parameters.

I am using  gromos 96 force field (G43a1) and as per your suggestion I have
edited the lipid.itp file to remove the part containing " lipid-gromos
interactions".


Thanking you,

Yours sincerely,
Pawan
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Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Before inserting the protein the bilayer was alright as I took the
equilibrated bilayer from Dr. Tieleman's website.
I have done the position restraint mdrun by restraining the protein only. In
this case also the lipids pull apart.

Thanking you,
Pawan

On Mon, Apr 6, 2009 at 1:33 PM, Kukol, Andreas  wrote:

> There is nothing wrong with the number of steps and the step size of 2 fs.
> Can you attach/send the coordinates of your system after position restraint
> MD ?
>
> What about your bilayer before inserting the protein ?  Does it move apart
> during MD ?
>
> Definetly you should perform another position restraint MD, restraining the
> protein only.
>
> Andreas
>
> >>>>>>>>>>>>>>>>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Pawan Kumar
> Sent: 06 April 2009 08:51
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
>
> Respected Sir,
>
> Greetings from Pawan.
> Thanks for your reply.
> After the position restraint mdrun the system looked quite justified as I
> restrained both the protein and the lipids.
> Is it because of the lesser number of steps ? I use 5000 steps with dt
> value of 0.002.
>
> Thanking you,
> Pawan
> On Mon, Apr 6, 2009 at 1:11 PM, Kukol, Andreas 
> wrote:
> Apparently the final mdrun has not worked successfully. It would be
> interesting to see what the system looks like after the position restraint
> mdrun.
>
> Andreas
>
> >>>>>>>>>>>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Pawan Kumar
> Sent: 06 April 2009 07:47
> To: Discussion list for GROMACS users; jalem...@vt.edu
> Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
>
> Respected Sir,
>
> Greetings from Pawan.
> Thanks for all your suggestions and help.
> The solvation is completed and the system is neutralized.
> The position restraint mdrun and final mdrun has worked out successfully
> without any warnings and errors this time.
> The structure after the final mdrun is not quite acceptable as the lipids
> have pulled apart and there is a huge gap between the two layers of the
> lipids. I have made the run for 5000 steps with dt = 0.002.
> Any suggestions please.
>
> Thanking you,
>
> Yours sincerely,
> Pawan
> On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul  wrote:
>
>
> Pawan Kumar wrote:
> Respected Sir,
>
> Greetings from Pawan.
> Thanks for all your kind help and suggestions.
> I will work on this and ask you if I have further doubts.
> Is it fine if I use the perl code given in
> wiki.gromacs.org/membrane-simulations <
> http://wiki.gromacs.org/membrane-simulations> for solvation after the
> genbox step to remove extra waters from the hydrophobic part of the bilayer
> ?
>
> You mean the C program or shell script at
> http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of
> those should be fine.
>
> -Justin
> Thanking you,
>
> Yours sincerely,
> Pawan
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for your reply.
After the position restraint mdrun the system looked quite justified as I
restrained both the protein and the lipids.
Is it because of the lesser number of steps ? I use 5000 steps with dt value
of 0.002.

Thanking you,
Pawan

On Mon, Apr 6, 2009 at 1:11 PM, Kukol, Andreas  wrote:

> Apparently the final mdrun has not worked successfully. It would be
> interesting to see what the system looks like after the position restraint
> mdrun.
>
> Andreas
>
> >>>>>>>>>>>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Pawan Kumar
> Sent: 06 April 2009 07:47
> To: Discussion list for GROMACS users; jalem...@vt.edu
> Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
>
> Respected Sir,
>
> Greetings from Pawan.
> Thanks for all your suggestions and help.
> The solvation is completed and the system is neutralized.
> The position restraint mdrun and final mdrun has worked out successfully
> without any warnings and errors this time.
> The structure after the final mdrun is not quite acceptable as the lipids
> have pulled apart and there is a huge gap between the two layers of the
> lipids. I have made the run for 5000 steps with dt = 0.002.
> Any suggestions please.
>
> Thanking you,
>
> Yours sincerely,
> Pawan
> On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul  wrote:
>
>
> Pawan Kumar wrote:
> Respected Sir,
>
> Greetings from Pawan.
> Thanks for all your kind help and suggestions.
> I will work on this and ask you if I have further doubts.
> Is it fine if I use the perl code given in
> wiki.gromacs.org/membrane-simulations <
> http://wiki.gromacs.org/membrane-simulations> for solvation after the
> genbox step to remove extra waters from the hydrophobic part of the bilayer
> ?
>
> You mean the C program or shell script at
> http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of
> those should be fine.
>
> -Justin
> Thanking you,
>
> Yours sincerely,
> Pawan
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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Re: [gmx-users] NEUTRALISED CHARGES

[Pawan Kumar]

Hi,

You should add 14 cl ions.

Regards,
Pawan

On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi <
bissoyi.akala...@gmail.com> wrote:

> hello gromacs
> i am trying to minimise my protein-ligand complex in gromacs.but it shows
> that system has non zero charge
> can any body says how much *cl ion*, i have to add to neutralised it. i am
> terminal window text.
> thank u
> --
> AKALABYA BISSOYI
> N.I.T.Rourkela
>
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for all your suggestions and help.
The solvation is completed and the system is neutralized.
The position restraint mdrun and final mdrun has worked out successfully
without any warnings and errors this time.
The structure after the final mdrun is not quite acceptable as the lipids
have pulled apart and there is a huge gap between the two layers of the
lipids. I have made the run for 5000 steps with dt = 0.002.
Any suggestions please.

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Thanks for all your kind help and suggestions.
>> I will work on this and ask you if I have further doubts.
>> Is it fine if I use the perl code given in
>> wiki.gromacs.org/membrane-simulations <
>> http://wiki.gromacs.org/membrane-simulations> for solvation after the
>> genbox step to remove extra waters from the hydrophobic part of the bilayer
>> ?
>>
>>
> You mean the C program or shell script at
> http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of
> those should be fine.
>
> -Justin
>
>  Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>>
>
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for your information.

Thanking you,
Pawan



On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Thanks for all your kind help and suggestions.
>> I will work on this and ask you if I have further doubts.
>> Is it fine if I use the perl code given in
>> wiki.gromacs.org/membrane-simulations <
>> http://wiki.gromacs.org/membrane-simulations> for solvation after the
>> genbox step to remove extra waters from the hydrophobic part of the bilayer
>> ?
>>
>>
> You mean the C program or shell script at
> http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of
> those should be fine.
>
> -Justin
>
>  Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>>
>
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Marc Sir,

Thanks for your information.

Thanking you,
Pawan

On Tue, Mar 31, 2009 at 5:31 PM, Marc F. Lensink wrote:

> On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote:
> >
> > Force fields have to be internally self-consistent, so using the
> parameters
> > from OPLS with Berger lipids will give spurious results.  The only proper
> > combinations are Gromos/Berger or OPLS/converted Berger.
>
> as long as one takes care of what one's doing, including proper
> validation, it's okay.  there is no one and unique lipid force field.
> berger parameters are directly derived from opls (see berger et al,
> biophys. j. 72 (1997), 2002).  they use the gromos combination rules
> but reduce the non-bonded 1,4 LJ by a factor of 8.  in any case,
> whatever you do, validation of the results is essential.  see also:
> http://pubs.acs.org/doi/abs/10.1021/la804150p
>
> cheers,
> marc
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in
wiki.gromacs.org/membrane-simulations for solvation after the genbox step to
remove extra waters from the hydrophobic part of the bilayer ?

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Thanks for all your suggestions.
>> Is it possible to use the lipid.itp file from Tieleman sir's website in
>> combination with GROMOS 96 force field without any modification ?
>>
>
> If you want to use lipid.itp without any modification, you are restricted
> to the ffgmx (deprecated!) force field.  For Gromos96-lipid.itp combination,
> simply remove the ";; parameters for lipid-GROMOS interactions," as these
> nonbonded combinations are for ffgmx only.  Otherwise, the nonbonded
> interactions (which now have consistent combination rules) should be
> generated correctly.
>
>  Is it fine if I use the Gromos/Berger force field combination for the
>> system I am using ?
>>
>
> That is a decision you will have to make based on a thorough examination of
> the literature, and the benefits and criticisms of these particular force
> field parameters.
>
>  I am sorry to ask this but can you please help me with some information
>> how to modify the lipid.itp file ?
>>
>
> That depends entirely upon what you want to do.  If you want Gromos/Berger,
> I've already told you.  If you want OPLS/modified Berger, search the
> archives for Chris Neale's posts on that topic.
>
> -Justin
>
>  I will edit vdwradii.dat file as per your suggestion.
>>
>>
>> Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Pawan Kumar wrote:
>>
>>Respected Sir,
>>
>>Greetings from Pawan.
>>I have edited the lipid.itp file to add just one line extra " H
>>atom from the opls_force_filed.itp " at the end of lipid
>>interactions data and that works fine.
>>I have done this after seeing the archives. It was given either
>>I should change the file for sigma and epsilon values or else
>>just add this line.
>>I think I have done it correctly. If not please correct me.
>>
>>
>>No, that is incorrect.  You need to add the additional atom type as
>>well as convert C6/C12 to sigma/epsilon.  Otherwise, the calculated
>>nonbonded interactions are meaningless.  Read instructions carefully!
>>
>>Force fields have to be internally self-consistent, so using the
>>parameters from OPLS with Berger lipids will give spurious results.
>> The only proper combinations are Gromos/Berger or OPLS/converted
>>Berger.
>>
>>
>>I have removed the position restraints after the inflategro
>>procedure.
>>After that I did energy minimization using define = -DFLEXIBLE.
>>I will change the temperature as per your suggestion.
>>I thought before solvating if I do position restraint mdrun the
>>lipids will compact more surrounding the protein.
>>
>>
>>No, your system will probably explode due to unsatisfied charge
>>interactions and hydrogen bonds.  There is a substantial dipole in
>>each lipid headgroup that can repel the lipids away from each other
>>if it is not shielded.
>>
>>
>>Thats the step when I got Lincs warnings and segmentation fault.
>>Then I tried solvating the system using genbox step and
>>spc216.gro as the solvent.
>>But before doing the solvation step I copied the vdwradii.dat
>>file into the working directory and increased the value for
>>carbon to 0.5.
>>But the result of this was " Segmentation fault " again. Can you
>>please tell me why I get the " Segmentation fault " here in this
>>step.
>>The command used was : genbox  -cp comp_em27.pdb -cs spc216.gro
>>-o box.pdb -p topol.top
>>
>>
>>    Using a 0.5-nm radius for carbon will cause problems of excess
>>memory consumption, or otherwise breaks the calculation.  Use
>>something more along the lines of 0.35 or 0.375, and manually delete
>>out any stray waters in the hydrophobic 

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's website in
combination with GROMOS 96 force field without any modification ?
Is it fine if I use the Gromos/Berger force field combination for the system
I am using ?
I am sorry to ask this but can you please help me with some information how
to modify the lipid.itp file ?
I will edit vdwradii.dat file as per your suggestion.

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I have edited the lipid.itp file to add just one line extra " H atom from
>> the opls_force_filed.itp " at the end of lipid interactions data and that
>> works fine.
>> I have done this after seeing the archives. It was given either I should
>> change the file for sigma and epsilon values or else just add this line.
>> I think I have done it correctly. If not please correct me.
>>
>
> No, that is incorrect.  You need to add the additional atom type as well as
> convert C6/C12 to sigma/epsilon.  Otherwise, the calculated nonbonded
> interactions are meaningless.  Read instructions carefully!
>
> Force fields have to be internally self-consistent, so using the parameters
> from OPLS with Berger lipids will give spurious results.  The only proper
> combinations are Gromos/Berger or OPLS/converted Berger.
>
>  I have removed the position restraints after the inflategro procedure.
>> After that I did energy minimization using define = -DFLEXIBLE.
>> I will change the temperature as per your suggestion.
>> I thought before solvating if I do position restraint mdrun the lipids
>> will compact more surrounding the protein.
>>
>
> No, your system will probably explode due to unsatisfied charge
> interactions and hydrogen bonds.  There is a substantial dipole in each
> lipid headgroup that can repel the lipids away from each other if it is not
> shielded.
>
>  Thats the step when I got Lincs warnings and segmentation fault.
>> Then I tried solvating the system using genbox step and spc216.gro as the
>> solvent.
>> But before doing the solvation step I copied the vdwradii.dat file into
>> the working directory and increased the value for carbon to 0.5.
>> But the result of this was " Segmentation fault " again. Can you please
>> tell me why I get the " Segmentation fault " here in this step.
>> The command used was : genbox  -cp comp_em27.pdb -cs spc216.gro -o box.pdb
>> -p topol.top
>>
>
> Using a 0.5-nm radius for carbon will cause problems of excess memory
> consumption, or otherwise breaks the calculation.  Use something more along
> the lines of 0.35 or 0.375, and manually delete out any stray waters in the
> hydrophobic core.
>
> -Justin
>
>>
>> Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Justin A. Lemkul wrote:
>>
>>
>>
>>Pawan Kumar wrote:
>>
>>Respected Sir,
>>
>>Greetings from Pawan.
>>I have used force constants of 10 in position restraint
>>.itp files for proteins as suggested in Dr. Tieleman' s
>>webisite for Inflategro.
>>The mdp files are :
>>
>>
>>The .mdp files look reasonable enough, although I don't know why
>>you are applying position restraints during EM.  If it is for
>>InflateGRO, that is fine, but once the system is assembled, you
>>should remove the position restraints from the protein to
>>minimize the system more.
>>
>>And are you sure you want 300K?  DPPC will be in a gel phase at
>>that temperature.  If you want a more realistic fluid-phase
>>model, you'll have to go above 315K (323K is common).
>>
>>
>>One thing I just noticed.  You don't have solvent in your
>>position-restrained run?  That could be a big problem if the lipid
>>headgroups are strongly repelled from one another.  Add solvent
>>before doing anything other than EM.
>>
>>-Justin
>>
>>
>>*Topology file :*
>>; Include forcefield parameters
>>#include "ffoplsaa.itp"
>>#include "lipid.itp"
>>#include "dppc.itp"
>>
>>
>>This section should

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I have edited the lipid.itp file to add just one line extra " H atom from
the opls_force_filed.itp " at the end of lipid interactions data and that
works fine.
I have done this after seeing the archives. It was given either I should
change the file for sigma and epsilon values or else just add this line.
I think I have done it correctly. If not please correct me.
I have removed the position restraints after the inflategro procedure.
After that I did energy minimization using define = -DFLEXIBLE.
I will change the temperature as per your suggestion.
I thought before solvating if I do position restraint mdrun the lipids will
compact more surrounding the protein.
Thats the step when I got Lincs warnings and segmentation fault.
Then I tried solvating the system using genbox step and spc216.gro as the
solvent.
But before doing the solvation step I copied the vdwradii.dat file into the
working directory and increased the value for carbon to 0.5.
But the result of this was " Segmentation fault " again. Can you please tell
me why I get the " Segmentation fault " here in this step.
The command used was : genbox  -cp comp_em27.pdb -cs spc216.gro -o box.pdb
-p topol.top

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul  wrote:

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Pawan Kumar wrote:
>>
>>> Respected Sir,
>>>
>>> Greetings from Pawan.
>>> I have used force constants of 10 in position restraint .itp files
>>> for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
>>> The mdp files are :
>>>
>>
>> The .mdp files look reasonable enough, although I don't know why you are
>> applying position restraints during EM.  If it is for InflateGRO, that is
>> fine, but once the system is assembled, you should remove the position
>> restraints from the protein to minimize the system more.
>>
>> And are you sure you want 300K?  DPPC will be in a gel phase at that
>> temperature.  If you want a more realistic fluid-phase model, you'll have to
>> go above 315K (323K is common).
>>
>>
> One thing I just noticed.  You don't have solvent in your
> position-restrained run?  That could be a big problem if the lipid
> headgroups are strongly repelled from one another.  Add solvent before doing
> anything other than EM.
>
> -Justin
>
>
>  *Topology file :*
>>> ; Include forcefield parameters
>>> #include "ffoplsaa.itp"
>>> #include "lipid.itp"
>>> #include "dppc.itp"
>>>
>>>
>> This section should not work, as written.  Have you modified lipid.itp
>> according to Chris Neale's half-epsilon double-pairlist method?  If not,
>> what you've done makes no sense.  The Berger lipid parameters distributed
>> through Tieleman's site are designed for use with the Gromos force fields.
>>  They can be modified (search in the archives), but that can also be a
>> source of error.  Users who have made mistakes in the conversion have seen
>> their systems explode.
>>
>> -Justin
>>
>>  ; Include chain topologies
>>> #include "topol_A.itp"
>>> #include "topol_B.itp"
>>> #include "topol_C.itp"
>>>
>>> ;#ifdef POSRES
>>> ;#include "lipid_posre.itp"
>>> ;#endif
>>>
>>> ; Include water topology
>>> #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 ]
>>> ; Name
>>> PROTEIN IN DPPC BILAYER
>>>
>>> [ molecules ]
>>> ; Compound  #mols
>>> Protein_A   1
>>> Protein_B   1
>>> Protein_C   1
>>> DPPC  926
>>> ;SOL 23552
>>>
>>> Please help with some suggestions.
>>>
>>> Thanking you,
>>>
>>> Yours sincerely,
>>> Pawan
>>>
>>> On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>Pawan Kumar wrote:
>>>
>>>Respected Sir,
>>>
>>

Re: [gmx-users] problem in simulation of lipid bilayer

[Pawan Kumar]

Dear Nitu madam,

You can directly go for simulation of lipid+protein complex if u r using a
pre-equilibrated bilayer as from Dr. Tieleman's website.

Regards,
Pawan

2009/3/31 nitu sharma 

> Dear all,
>
>   I  am trying to simulation of membrane proteins  I have a
> basic question can we directly go for simulation of lipid+protein complex
> without doing simulation of individually simulation of lipid bilayer
> because  I am facing lot of problem with topology file for lipid bilayer .
>
> please any one suggest me whats the right thing I have to do.
>
>
> thanks.
>
> nitu sharma
> School of life Sciences
> Jawaherlal nehru university
> New delhi,India
>
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I have used force constants of 10 in position restraint .itp files for
proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
The mdp files are :

*For energy minimization:*
title   =  Protein in DPPC Bilayer
cpp =  /usr/bin/cpp
define  =  -DPOSRES
integrator  =  steep
dt  =  0.002
nsteps  =  5

; Constrain control
constraints =  none

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout =  0
nstvout =  0
nstfout =  0
nstxtcout   =  0
nstenergy   =  0

; nblist update frequency
nstlist =  10

; ns algorithm
ns_type =  grid
rlist   =  1.8

; Method for doing VdW
vdw-type=  Cut-off
rvdw=  1.8

; Method for doing electrostatics
coulombtype=  PME
rcoulomb=  1.8

; Center of mass control
nstcomm  =  1

; Periodic boundary conditions
pbc  =  xyz

; Mode for center of mass motion removal
comm-mode=  Linear

tcoupl   =  no
pcoupl   =  no
;   Energy minimizing stuff
emtol=  1000
emstep   =  0.001

*For position restraint mdrun:*
title   =  Protein in DPPC Bilayer
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
constraint-algorithm=  Lincs
integrator  =  md
dt  =  0.002
nsteps  =  5000
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  Cut-off
rvdw=  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps  =  Protein  DPPC
tau_t   =  0.10.1
ref_t   =  300300
; Energy monitoring
energygrps=  Protein DPPC
;Pressure coupling is on
Pcoupl  =  berendsen
tau_p   =  2.0 2.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529

*Topology file :*
; Include forcefield parameters
#include "ffoplsaa.itp"
#include "lipid.itp"
#include "dppc.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"

;#ifdef POSRES
;#include "lipid_posre.itp"
;#endif

; Include water topology
#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 ]
; Name
PROTEIN IN DPPC BILAYER

[ molecules ]
; Compound  #mols
Protein_A   1
Protein_B   1
Protein_C   1
DPPC  926
;SOL 23552

Please help with some suggestions.

Thanking you,

Yours sincerely,
Pawan

On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul  wrote:


> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I did the Inflategro procedure for the POPC bilayer generated using
>> genconf.
>> It took around 26 compressions for coming near the initial area (just
>> above it).
>> The minimization were all converged to Fmax < 1350.
>> If I decrease the Fmax less than this I am getting machine precision.
>> But when I proceeded with the final compressed structure for pr mdrun it
>> gave lincs warnings and ended with segmentation fault.
>> As an alternative to this bilayer I used the DPPC bilayer
>> (pre-equilibrated) which is given in GMX-Benchmark distribution.
>> I carried out the same steps of Inflategro. I used the cutoff of 14 A in
>> the inflation and compression step also.
>> In this case the the Steepest Descents converged to Fmax < 1000 in all the
>> steps. The maximum force war never above 850.
>> But when I did position restraint mdrun with the last compressed file I
>> got Lincs warnings and Segementation fault after few steps (30 - 40 steps).
>> Can you please help how to proceed ?
>>
>>
> If the minimization procedure is adequately finishing, then the problem
> comes from something you are doing.  If you post your .mdp file, we may be
> able to see if there are any obvious mistakes.
>
> -Justin
>
>  Thanki

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I did the Inflategro procedure for the POPC bilayer generated using genconf.
It took around 26 compressions for coming near the initial area (just above
it).
The minimization were all converged to Fmax < 1350.
If I decrease the Fmax less than this I am getting machine precision.
But when I proceeded with the final compressed structure for pr mdrun it
gave lincs warnings and ended with segmentation fault.
As an alternative to this bilayer I used the DPPC bilayer (pre-equilibrated)
which is given in GMX-Benchmark distribution.
I carried out the same steps of Inflategro. I used the cutoff of 14 A in the
inflation and compression step also.
In this case the the Steepest Descents converged to Fmax < 1000 in all the
steps. The maximum force war never above 850.
But when I did position restraint mdrun with the last compressed file I got
Lincs warnings and Segementation fault after few steps (30 - 40 steps).
Can you please help how to proceed ?

Thanking you,

Yours sincerely,
Pawan


On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I read in the manual about the freeze-grps but dint find a good
>> explanation about the usage.
>> Can you please tell me how to use freeze-grps in all dimensions during the
>> minimizations ?
>>
>>
> If you search for "freezegrps" within the list archive (the "Search"
> feature of the Gromacs homepage), you will find several hundred results,
> many of which provide examples of what users are trying and what may or may
> not work.  This should be instructive.
>
> In a general sense, freezegrps are just like anything else under the group
> theory in Gromacs.  Make an index group for the group of atoms you want to
> freeze (i.e., headgroups) and the dimensions in which you want them frozen
> (x, y, z - yes(Y) or no(N) for each).
>
> If you are choosing the route of POPE, it is very difficult to get these
> systems built using InflateGRO.  At least, that has been my experience.
>  Prepare to spend a lot of time with trial and error and very careful
> equilibration.
>
> -Justin
>
>  Thanking you,
>> Pawan
>>
>>On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul ><mailto:jalem...@vt.edu>> wrote:
>>
>>
>>Pawan Kumar wrote:
>>
>>Respected Sir,
>>
>>Thanks for all your help, suggestions and guidance.
>>I have few more queries.
>>Which type of box is appropriate in editconf - cubic or triclinic ?
>>
>>
>>That depends entirely upon the dimensions of your system and what is
>>adequate to accommodate the size of your embedded protein.
>>
>>
>>I have read in one of your mails in the archives that POPE
>>bilayer contains some bad interactions. As it contains more no.
>>of lipids (340) it covers the full protein ( trimer which I am
>>working on ) other than the few loop regions. How far that
>>bilayer can be used or is it fine to use the biger bilayer of
>>popc128a whcih I obtained by genconf ?
>>
>>
>>The choice of lipid should not be based on a size convenience.  It
>>should be based on a valid model system, and experimental evidence
>>to which you can correlate your results, if possible.
>>
>>POPE presented a terrible challenge, since during the in vacuo
>>InflateGRO minimizations, the headgroups folded in on themselves to
>>form intra-molecule hydrogen bonds that resulted in a collapse of
>>the molecule.  The solution was to use freeze-grps in all dimensions
>>during these minimizations, and then equilibrate very carefully.
>>
>>
>>
>>Justin A. Lemkul
>>Graduate Research Assistant
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
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>><mailto:gmx-users@gromacs.org>
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Re: [gmx-users] grompp error in running simulation of lipid bilayer

[Pawan Kumar]

Hello Madam,

Greetings from Pawan.
The solution for this is to edit the atom names as required such as replace
NTM  with N4 in all the places wherever NTM occurs.
Similarly do this for all the atoms of the dppc lipid.
I think this is a probable solution.
I dont know how far I am right.

Regards,
Pawan

2009/3/30 nitu sharma 

> Hi pawan ,
>
>   Thanks for your right suggestion bu t after editing lipid.itp the
> another error comes like this-
>
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Generated 1369 of the 2211 non-bonded parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/flexspc.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
> Excluding 3 bonded neighbours molecule type 'DMPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> Warning: atom name 1 in dmpc.top and dmpc-box.pdb does not match (CN1 - C1)
> Warning: atom name 2 in dmpc.top and dmpc-box.pdb does not match (CN2 - C2)
> Warning: atom name 3 in dmpc.top and dmpc-box.pdb does not match (CN3 - C3)
> Warning: atom name 4 in dmpc.top and dmpc-box.pdb does not match (NTM - N4)
> Warning: atom name 5 in dmpc.top and dmpc-box.pdb does not match (CA - C5)
> Warning: atom name 6 in dmpc.top and dmpc-box.pdb does not match (CB - C6)
> Warning: atom name 7 in dmpc.top and dmpc-box.pdb does not match (OA - O7)
> Warning: atom name 8 in dmpc.top and dmpc-box.pdb does not match (P - P8)
> Warning: atom name 9 in dmpc.top and dmpc-box.pdb does not match (OB - O9)
> Warning: atom name 10 in dmpc.top and dmpc-box.pdb does not match (OC -
> O10)
> Warning: atom name 11 in dmpc.top and dmpc-box.pdb does not match (OD -
> O11)
> Warning: atom name 12 in dmpc.top and dmpc-box.pdb does not match (CC -
> C12)
> Warning: atom name 13 in dmpc.top and dmpc-box.pdb does not match (CD -
> C13)
> Warning: atom name 14 in dmpc.top and dmpc-box.pdb does not match (OE -
> O14)
> Warning: atom name 15 in dmpc.top and dmpc-box.pdb does not match (C2A -
> C15)
> Warning: atom name 16 in dmpc.top and dmpc-box.pdb does not match (OF -
> O16)
> Warning: atom name 17 in dmpc.top and dmpc-box.pdb does not match (C2B -
> C17)
> Warning: atom name 18 in dmpc.top and dmpc-box.pdb does not match (C2C -
> C18)
> Warning: atom name 19 in dmpc.top and dmpc-box.pdb does not match (C2D -
> C19)
> Warning: atom name 20 in dmpc.top and dmpc-box.pdb does not match (C2E -
> C20)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file dmpc.top, line 20]:
>   5888 non-matching atom names
>   atom names from dmpc.top will be used
>   atom names from dmpc-box.pdb will be ignored
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are:  3783  OTHER residues
> There are: 0PROTEIN residues
> There are: 0DNA residues
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 16853 elements
> Making dummy/rest group for Acceleration containing 16853 elements
> Making dummy/rest group for Freeze containing 16853 elements
> Making dummy/rest group for Energy Mon. containing 16853 elements
> Making dummy/rest group for VCM containing 16853 elements
> Number of degrees of freedom in T-Coupling group rest is 50556.00
> Making dummy/rest group for User1 containing 16853 elements
> Making dummy/rest group for User2 containing 16853 elements
> Making dummy/rest group for XTC containing 16853 elements
> Making dummy/rest group for Or. Res. Fit containing 16853 elements
> Making dummy/rest group for QMMM containing 16853 elements
> T-Coupling   has 1 element(s): rest
> Energy Mon.  has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze   has 1 element(s): rest
> User1has 1 element(s): rest
> User2has 1 element(s): rest
> VCM  has 1 element(s): rest
> XTC  has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> NOTE 1 [file em.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, this will often produce artifacts.
>   You might want to consider using PME electrostatics.
>
>
> This run will generate roughly 2 Mb of data
> writing run input file...
>
> There was 1 note
>
> There was 1 warning
>
> ---
> Program grompp, VERSION 4.0.3
> Source code file: gmx_fatal.c, line: 481
>
> Fatal error:
> Too many warnings (1), grompp terminated.
> If

Re: [gmx-users] grompp error in running simulation of lipid bilayer

[Pawan Kumar]

Hi,

Greetings from Pawan.
Edit your lipid.itp file.
Comment or remove the lines :
   [default]
   1   1

Then grompp will work..

Regards,
Pawan

2009/3/30 nitu sharma 

> Dear all ,
>
>
> I am trying to do simulation of  DMPC lipid
> bilayer  for this I have made topology file with the help of teleman
> website  by downloading two file -lipid.itp &dmpc.itp . But when I run the
> grompp  for energy minimisation I am getting error like this -
>
> Program grompp, VERSION 4.0.3
> Source code file: topio.c, line: 430
>
> Fatal error:
> Syntax error - File lipid.itp, line 9
> Last line read:
> '1   1'
> Found a second defaults directive.
>
> my command line like this- [n...@localhost dmpc1tap]$ grompp -f em.mdp  -p
> dmpc.top  -c   dmpc-solvated.pdb -o  dmpc-em.tpr
> If anyone know about this please help me in solving this problem .
>
> its very useful for me.
>
> thank you very much in advance.
>
> Nitu Sharma
> School Of life sciences
> Jawaherlal Nehru University
> New Delhi, India
>
>
>
>
> ___
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Thanks for your help and suggestions.
First I will try to use POPC (the one generated using genconf) . If it
doesnt work then I will switch over to POPE.
I will ask you if I have any further queries.

Thanking you,
Pawan


On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I read in the manual about the freeze-grps but dint find a good
>> explanation about the usage.
>> Can you please tell me how to use freeze-grps in all dimensions during the
>> minimizations ?
>>
>>
> If you search for "freezegrps" within the list archive (the "Search"
> feature of the Gromacs homepage), you will find several hundred results,
> many of which provide examples of what users are trying and what may or may
> not work.  This should be instructive.
>
> In a general sense, freezegrps are just like anything else under the group
> theory in Gromacs.  Make an index group for the group of atoms you want to
> freeze (i.e., headgroups) and the dimensions in which you want them frozen
> (x, y, z - yes(Y) or no(N) for each).
>
> If you are choosing the route of POPE, it is very difficult to get these
> systems built using InflateGRO.  At least, that has been my experience.
>  Prepare to spend a lot of time with trial and error and very careful
> equilibration.
>
> -Justin
>
>  Thanking you,
>> Pawan
>>
>>On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul ><mailto:jalem...@vt.edu>> wrote:
>>
>>
>>Pawan Kumar wrote:
>>
>>Respected Sir,
>>
>>Thanks for all your help, suggestions and guidance.
>>I have few more queries.
>>Which type of box is appropriate in editconf - cubic or triclinic ?
>>
>>
>>That depends entirely upon the dimensions of your system and what is
>>adequate to accommodate the size of your embedded protein.
>>
>>
>>I have read in one of your mails in the archives that POPE
>>bilayer contains some bad interactions. As it contains more no.
>>of lipids (340) it covers the full protein ( trimer which I am
>>working on ) other than the few loop regions. How far that
>>bilayer can be used or is it fine to use the biger bilayer of
>>popc128a whcih I obtained by genconf ?
>>
>>
>>The choice of lipid should not be based on a size convenience.  It
>>should be based on a valid model system, and experimental evidence
>>to which you can correlate your results, if possible.
>>
>>POPE presented a terrible challenge, since during the in vacuo
>>InflateGRO minimizations, the headgroups folded in on themselves to
>>form intra-molecule hydrogen bonds that resulted in a collapse of
>>the molecule.  The solution was to use freeze-grps in all dimensions
>>during these minimizations, and then equilibrate very carefully.
>>
>>
>>
>>Justin A. Lemkul
>>Graduate Research Assistant
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>><mailto: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
>>gmx-users-requ...@gromacs.org
>><mailto:gmx-users-requ...@gromacs.org>.
>>Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>>
> --
> 
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gro

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I read in the manual about the freeze-grps but dint find a good explanation
about the usage.
Can you please tell me how to use freeze-grps in all dimensions during the
minimizations ?

Thanking you,
Pawan

> On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul  wrote:
>
>

> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Thanks for all your help, suggestions and guidance.
>> I have few more queries.
>> Which type of box is appropriate in editconf - cubic or triclinic ?
>>
>
> That depends entirely upon the dimensions of your system and what is
> adequate to accommodate the size of your embedded protein.
>
>  I have read in one of your mails in the archives that POPE bilayer
>> contains some bad interactions. As it contains more no. of lipids (340) it
>> covers the full protein ( trimer which I am working on ) other than the few
>> loop regions. How far that bilayer can be used or is it fine to use the
>> biger bilayer of popc128a whcih I obtained by genconf ?
>>
>>
> The choice of lipid should not be based on a size convenience.  It should
> be based on a valid model system, and experimental evidence to which you can
> correlate your results, if possible.
>
> POPE presented a terrible challenge, since during the in vacuo InflateGRO
> minimizations, the headgroups folded in on themselves to form intra-molecule
> hydrogen bonds that resulted in a collapse of the molecule.  The solution
> was to use freeze-grps in all dimensions during these minimizations, and
> then equilibrate very carefully.
>
>
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://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 gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>
___
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[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Thanks for all your help.
I will try this out and if I have any further queries I will ask you.
Thanks a lot.

Thanking you,
Pawan

On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul  wrote:


Pawan Kumar wrote:

> Respected Sir,
>
> Thanks for all your help, suggestions and guidance.
> I have few more queries.
> Which type of box is appropriate in editconf - cubic or triclinic ?
>

That depends entirely upon the dimensions of your system and what is
adequate to accommodate the size of your embedded protein.

 I have read in one of your mails in the archives that POPE bilayer contains
> some bad interactions. As it contains more no. of lipids (340) it covers the
> full protein ( trimer which I am working on ) other than the few loop
> regions. How far that bilayer can be used or is it fine to use the biger
> bilayer of popc128a whcih I obtained by genconf ?
>
>
The choice of lipid should not be based on a size convenience.  It should be
based on a valid model system, and experimental evidence to which you can
correlate your results, if possible.

POPE presented a terrible challenge, since during the in vacuo InflateGRO
minimizations, the headgroups folded in on themselves to form intra-molecule
hydrogen bonds that resulted in a collapse of the molecule.  The solution
was to use freeze-grps in all dimensions during these minimizations, and
then equilibrate very carefully.


>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://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 gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
___
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Thanks for all your help, suggestions and guidance.
I have few more queries.
Which type of box is appropriate in editconf - cubic or triclinic ?
I have read in one of your mails in the archives that POPE bilayer contains
some bad interactions. As it contains more no. of lipids (340) it covers the
full protein ( trimer which I am working on ) other than the few loop
regions. How far that bilayer can be used or is it fine to use the biger
bilayer of popc128a whcih I obtained by genconf ?

Thanking you,
Pawan
___
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for your reply.
I used to do genbox first and then Inflategro all the time.
Is it possible to concatenate one file after the other using " vi editor" -
I mean just copying the contents of the membrane.gro file at the end of
protein.gro file ?
Is it fine if I generate the .gro files using editconf command ?
Thanks for your kind help.

Thanking you,
Pawan

On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> Thanks for your mail.
>> I will tell you in detail.
>> The control lipid bilayer ( which is generated using genconf -nbox 2 2 1
>> -dist 0 0 0 ) minimized fine with an emtol value of 1510.
>> Then after inserting the protein with genbox the whole system minimized
>> with an emtol value of 2250.
>> Then I am trying to do position restraint mdrun where I am getting errors.
>> Inflategro can be used only after inserting the protein right (which I did
>> using genbox with -vdwd option as 0.6) ?
>>
>>
> No.  Read the documentation carefully.  You first concatenate your protein
> and membrane .gro files, then use InflateGRO on that system.  There is no
> genbox involved when using InflateGRO, hence why I suggested it as a
> (potentially) more reliable method.
>
> -Justin
>
>  Thanking you,
>> Pawan
>>
>> On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Pawan Kumar wrote:
>>
>>Hello Justin Sir,
>>
>>Greetings from Pawan.
>>Sorry for the inconvenience.
>>Next time I will keep in mind about the subject line.
>>I tried deleting those particular atoms where it gave the
>>maximum force.
>>
>>
>>You said that this atom was part of a lipid.  Deleting these atoms
>>will give you a broken structure and an unrealistic system.  It
>>should also cause grompp to complain.
>>
>>
>>But every time a new atom with a maximum force was given in the
>>output.
>>Is it fine to use to use "constraints = all-angles" in order to
>>overcome the Lincs warnings ?
>>
>>
>>No.  LINCS warnings indicate that there is something fundamentally
>>wrong with your system.  It likely stems from how you inserted your
>>protein into the lipids.  Think about it.  Your control lipid
>>bilayer minimized fine.  Your protein-membrane system does not, if
>>that is what we're still talking about. That indicates to me that
>>the problem is not with the lipids, the problem is with the
>>insertion of the protein.
>>
>>Instead of genbox (which is somewhat crude), try the InflateGRO
>>script from Tieleman's site.  I have used it many times to build
>>nicely-packed membrane protein systems.  It takes substantially
>>longer to build the system than with genbox, but I think the results
>>are more reliable.
>>
>>-Justin
>>
>>Thanks in advance.
>>
>>Thanking you,
>>Pawan
>>
>>
>>
>>
>>On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>   When replying to digests, please change the subject line to
>>   something relevant.
>>
>>   Pawan Kumar wrote:
>>
>>   Hello Justin Sir,
>>
>>   Greetings from Pawan.
>>   Sorry for the late reply.
>>   The max. force was 1.2447973e+o5 on atom 19448.
>>
>>
>>   An Fmax that high is sure to generate problems.  It is up to
>>you to
>>   inspect your system, understand which atoms are interacting
>>to cause
>>   such a force, and determine if you've done something wrong.
>>
>>   -Justin
>>
>>   This particular atom belongs to one of the lipid residues
>>of the
>>   bilayer.
>>   I get Lincs warnings whenever I run the position
>>restraint mdrun.
>>
>>   Thanking you,
>>   Pawan
>>
>>
>>   On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul
>>   mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Thanks for your mail.
I will tell you in detail.
The control lipid bilayer ( which is generated using genconf -nbox 2 2 1
-dist 0 0 0 ) minimized fine with an emtol value of 1510.
Then after inserting the protein with genbox the whole system minimized with
an emtol value of 2250.
Then I am trying to do position restraint mdrun where I am getting errors.
Inflategro can be used only after inserting the protein right (which I did
using genbox with -vdwd option as 0.6) ?

Thanking you,
Pawan

On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Hello Justin Sir,
>>
>> Greetings from Pawan.
>> Sorry for the inconvenience.
>> Next time I will keep in mind about the subject line.
>> I tried deleting those particular atoms where it gave the maximum force.
>>
>
> You said that this atom was part of a lipid.  Deleting these atoms will
> give you a broken structure and an unrealistic system.  It should also cause
> grompp to complain.
>
>  But every time a new atom with a maximum force was given in the output.
>> Is it fine to use to use "constraints = all-angles" in order to overcome
>> the Lincs warnings ?
>>
>
> No.  LINCS warnings indicate that there is something fundamentally wrong
> with your system.  It likely stems from how you inserted your protein into
> the lipids.  Think about it.  Your control lipid bilayer minimized fine.
>  Your protein-membrane system does not, if that is what we're still talking
> about. That indicates to me that the problem is not with the lipids, the
> problem is with the insertion of the protein.
>
> Instead of genbox (which is somewhat crude), try the InflateGRO script from
> Tieleman's site.  I have used it many times to build nicely-packed membrane
> protein systems.  It takes substantially longer to build the system than
> with genbox, but I think the results are more reliable.
>
> -Justin
>
>  Thanks in advance.
>>
>> Thanking you,
>> Pawan
>>
>>
>>
>>
>> On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>When replying to digests, please change the subject line to
>>something relevant.
>>
>>Pawan Kumar wrote:
>>
>>Hello Justin Sir,
>>
>>Greetings from Pawan.
>>Sorry for the late reply.
>>The max. force was 1.2447973e+o5 on atom 19448.
>>
>>
>>An Fmax that high is sure to generate problems.  It is up to you to
>>inspect your system, understand which atoms are interacting to cause
>>such a force, and determine if you've done something wrong.
>>
>>-Justin
>>
>>This particular atom belongs to one of the lipid residues of the
>>bilayer.
>>I get Lincs warnings whenever I run the position restraint mdrun.
>>
>>Thanking you,
>>Pawan
>>
>>
>>On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   Pawan Kumar wrote:
>>
>>   Hello Justin Sir,
>>
>>   Greetings from Pawan
>>   Thanks for your valuable suggestion and reply.
>>   Initially I gave the emtol of 1000 and the output I got was
>> :
>>   Steepest Descents converged to machine precision in 163
>> steps
>>   but did not reach the requested Fmax<1000.
>>   Potential Energy = - 4.4516497e+05
>>
>>
>>   ...and how close did Fmax get to 1000?
>>
>>
>>   Even I tried to minimize the popc bilayer which I took from
>>   Tieleman sir's website ( before generating a bigger bilayer
>>   using genconf ) but that also converged to machine
>>precision but
>>   not to the requested Fmax<1000. How do I proceed further ?
>>
>>
>>   Well, these things are not absolute; Fmax = 1000 is kind of a
>>rule
>>   of thumb that I use in my own work, but sometimes it is not
>>   necessary.  Careful equilibration should massage your system
>> into
>>   cooperating.
>>
>>   -Justin
>>
>>   Thanks for your suggestions and help.
>>
>>   Thanking you,
>>   Pawan
>>
>>   On Thu, Mar 19, 2009 at 9:13 PM,
>>
>> 

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hello Justin Sir,

Greetings from Pawan.
Sorry for the inconvenience.
Next time I will keep in mind about the subject line.
I tried deleting those particular atoms where it gave the maximum force.
But every time a new atom with a maximum force was given in the output.
Is it fine to use to use "constraints = all-angles" in order to overcome the
Lincs warnings ?
Thanks in advance.

Thanking you,
Pawan




On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul  wrote:

>
> When replying to digests, please change the subject line to something
> relevant.
>
> Pawan Kumar wrote:
>
>> Hello Justin Sir,
>>
>> Greetings from Pawan.
>> Sorry for the late reply.
>> The max. force was 1.2447973e+o5 on atom 19448.
>>
>
> An Fmax that high is sure to generate problems.  It is up to you to inspect
> your system, understand which atoms are interacting to cause such a force,
> and determine if you've done something wrong.
>
> -Justin
>
>  This particular atom belongs to one of the lipid residues of the bilayer.
>> I get Lincs warnings whenever I run the position restraint mdrun.
>>
>> Thanking you,
>> Pawan
>>
>>
>> On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Pawan Kumar wrote:
>>
>>Hello Justin Sir,
>>
>>Greetings from Pawan
>>Thanks for your valuable suggestion and reply.
>>Initially I gave the emtol of 1000 and the output I got was :
>>Steepest Descents converged to machine precision in 163 steps
>>but did not reach the requested Fmax<1000.
>>Potential Energy = - 4.4516497e+05
>>
>>
>>...and how close did Fmax get to 1000?
>>
>>
>>Even I tried to minimize the popc bilayer which I took from
>>Tieleman sir's website ( before generating a bigger bilayer
>>using genconf ) but that also converged to machine precision but
>>not to the requested Fmax<1000. How do I proceed further ?
>>
>>
>>Well, these things are not absolute; Fmax = 1000 is kind of a rule
>>of thumb that I use in my own work, but sometimes it is not
>>necessary.  Careful equilibration should massage your system into
>>cooperating.
>>
>>-Justin
>>
>>Thanks for your suggestions and help.
>>
>>Thanking you,
>>Pawan
>>
>>On Thu, Mar 19, 2009 at 9:13 PM,
>>
>>   Pawan Kumar wrote:
>>> Hello Justin Sir,
>>>
>>> Greetings from Pawan
>>> Thanks for your valuable suggestion and reply.
>>> After inserting the protein in the bilayer using genbox I
>> have
>>   minimized
>>> the whole system without using any position restraints
>>(i.e. define =
>>> -DFLEXIBLE in em.mdp file). I used vanderwaal's distance
>>parameter (
>>> -vdwd of 0.6 ) in the genbox step.
>>> After running mdrun for energy minimization I got the
>>output as :
>>> Steepest Descents converged to Fmax<2250 in 14 steps.
>>> Potential energy = - 6.9484700e+05
>>> Maximum force = 2.2114819e+03 on atom 34277
>>> Norm. of force = 5.0103039e+04
>>>
>>
>>   You should try for an Fmax of no greater than 1000.  2250 is
>>still
>>   very high.
>>
>>> I tried decreasing the emtol value in the em.mdp file but it
>>   ended with
>>> machine precision.
>>
>>   How far did it converge?  What was Fmax?
>>
>>> I have read in literature that 5000 steps of Steetest
>>Descents run is
>>> required after inserting the protein in the bilayer which
>>should be
>>> followed by atleast 1000 steps of conjugate gradients. How
>>can I
>>> accomplish this ? Is there any parameter to be given in the
>>   em.mdp file
>>> ? I use steep as the integrator in the mdp file for energy
>>   minimization.
>>
>>   Read the manual.
>>
>>   Whether or not that exact setup is going to be "required" is
>>likely
>>   system-specific.  I would say that as long as your system
>>converges
>>   to a s

Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138

[Pawan Kumar]

Hello Justin Sir,

Greetings from Pawan.
Sorry for the late reply.
The max. force was 1.2447973e+o5 on atom 19448.
This particular atom belongs to one of the lipid residues of the bilayer.
I get Lincs warnings whenever I run the position restraint mdrun.

Thanking you,
Pawan


On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul  wrote:

>
>
> Pawan Kumar wrote:
>
>> Hello Justin Sir,
>>
>> Greetings from Pawan
>> Thanks for your valuable suggestion and reply.
>> Initially I gave the emtol of 1000 and the output I got was :
>> Steepest Descents converged to machine precision in 163 steps but did not
>> reach the requested Fmax<1000.
>> Potential Energy = - 4.4516497e+05
>>
>>
> ...and how close did Fmax get to 1000?
>
>  Even I tried to minimize the popc bilayer which I took from Tieleman sir's
>> website ( before generating a bigger bilayer using genconf ) but that also
>> converged to machine precision but not to the requested Fmax<1000. How do I
>> proceed further ?
>>
>
> Well, these things are not absolute; Fmax = 1000 is kind of a rule of thumb
> that I use in my own work, but sometimes it is not necessary.  Careful
> equilibration should massage your system into cooperating.
>
> -Justin
>
>  Thanks for your suggestions and help.
>>
>> Thanking you,
>> Pawan
>>
>> On Thu, Mar 19, 2009 at 9:13 PM,
>>
>>Pawan Kumar wrote:
>> > Hello Justin Sir,
>> >
>> > Greetings from Pawan
>> > Thanks for your valuable suggestion and reply.
>> > After inserting the protein in the bilayer using genbox I have
>>minimized
>> > the whole system without using any position restraints (i.e. define
>> =
>> > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter (
>> > -vdwd of 0.6 ) in the genbox step.
>> > After running mdrun for energy minimization I got the output as :
>> > Steepest Descents converged to Fmax<2250 in 14 steps.
>> > Potential energy = - 6.9484700e+05
>> > Maximum force = 2.2114819e+03 on atom 34277
>> > Norm. of force = 5.0103039e+04
>> >
>>
>>You should try for an Fmax of no greater than 1000.  2250 is still
>>very high.
>>
>> > I tried decreasing the emtol value in the em.mdp file but it
>>ended with
>> > machine precision.
>>
>>How far did it converge?  What was Fmax?
>>
>> > I have read in literature that 5000 steps of Steetest Descents run
>> is
>> > required after inserting the protein in the bilayer which should be
>> > followed by atleast 1000 steps of conjugate gradients. How can I
>> > accomplish this ? Is there any parameter to be given in the
>>em.mdp file
>> > ? I use steep as the integrator in the mdp file for energy
>>minimization.
>>
>>Read the manual.
>>
>>Whether or not that exact setup is going to be "required" is likely
>>system-specific.  I would say that as long as your system converges
>>to a stable,
>>negative Epot with a reasonable Fmax (less than 1000, but ideally
>>lower) then
>>you *may* have an appropriate starting structure.
>>
>>-Justin
>>
>> > Please help with some suggestions.
>> > Thanks in advance.
>> >
>> > Thanking you,
>> > Pawan
>> >
>> >
>> >
>>
>>
>>
>> 
>>
>> ___
>> 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!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138

[Pawan Kumar]

Hello Justin Sir,

Greetings from Pawan
Thanks for your valuable suggestion and reply.
Initially I gave the emtol of 1000 and the output I got was :
Steepest Descents converged to machine precision in 163 steps but did not
reach the requested Fmax<1000.
Potential Energy = - 4.4516497e+05

Even I tried to minimize the popc bilayer which I took from Tieleman sir's
website ( before generating a bigger bilayer using genconf ) but that also
converged to machine precision but not to the requested Fmax<1000. How do I
proceed further ?
Thanks for your suggestions and help.

Thanking you,
Pawan

On Thu, Mar 19, 2009 at 9:13 PM,

> Pawan Kumar wrote:
> > Hello Justin Sir,
> >
> > Greetings from Pawan
> > Thanks for your valuable suggestion and reply.
> > After inserting the protein in the bilayer using genbox I have minimized
> > the whole system without using any position restraints (i.e. define =
> > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter (
> > -vdwd of 0.6 ) in the genbox step.
> > After running mdrun for energy minimization I got the output as :
> > Steepest Descents converged to Fmax<2250 in 14 steps.
> > Potential energy = - 6.9484700e+05
> > Maximum force = 2.2114819e+03 on atom 34277
> > Norm. of force = 5.0103039e+04
> >
>
> You should try for an Fmax of no greater than 1000.  2250 is still very
> high.
>
> > I tried decreasing the emtol value in the em.mdp file but it ended with
> > machine precision.
>
> How far did it converge?  What was Fmax?
>
> > I have read in literature that 5000 steps of Steetest Descents run is
> > required after inserting the protein in the bilayer which should be
> > followed by atleast 1000 steps of conjugate gradients. How can I
> > accomplish this ? Is there any parameter to be given in the em.mdp file
> > ? I use steep as the integrator in the mdp file for energy minimization.
>
> Read the manual.
>
> Whether or not that exact setup is going to be "required" is likely
> system-specific.  I would say that as long as your system converges to a
> stable,
> negative Epot with a reasonable Fmax (less than 1000, but ideally lower)
> then
> you *may* have an appropriate starting structure.
>
> -Justin
>
> > Please help with some suggestions.
> > Thanks in advance.
> >
> > Thanking you,
> > Pawan
> >
> >
> >
>
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Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hello Justin Sir,

Greetings from Pawan
Thanks for your valuable suggestion and reply.
After inserting the protein in the bilayer using genbox I have minimized the
whole system without using any position restraints (i.e. define = -DFLEXIBLE
in em.mdp file). I used vanderwaal's distance parameter ( -vdwd of 0.6 ) in
the genbox step.
After running mdrun for energy minimization I got the output as :
Steepest Descents converged to Fmax<2250 in 14 steps.
Potential energy = - 6.9484700e+05
Maximum force = 2.2114819e+03 on atom 34277
Norm. of force = 5.0103039e+04

I tried decreasing the emtol value in the em.mdp file but it ended with
machine precision.
I have read in literature that 5000 steps of Steetest Descents run is
required after inserting the protein in the bilayer which should be followed
by atleast 1000 steps of conjugate gradients. How can I accomplish this ? Is
there any parameter to be given in the em.mdp file ? I use steep as the
integrator in the mdp file for energy minimization. Please help with some
suggestions.
Thanks in advance.

Thanking you,
Pawan



On Thu, Mar 19, 2009 at 5:41 PM,

> Pawan Kumar wrote:
> > Hello Justin Sir,
> >
> > Thanks for your reply.
> > I changed the dt value as per the suggestion.
> > But after 200 steps the same kind of warnings came  like "pressure
> > scaling more than 1%" and "1-4 interactions" and then it stopped after
> > writing few pdb files. Then I decreased the dt value still lesser
> > (0.1) and this time it continued with all the given steps but the
> > lipids' structure were distorted into small fragments.
>
> If your system is not properly energy-minimized, there is no change in dt
> that
> will help you.  Ensure that your EM converged to reasonable values of Epot
> and
> Fmax before continuing.
>
> > The other query I have is what should the optimal value for these
> > parameters for membrane proteins :  rlist, rcoulomb, and rvdw. I have
> > used the value of 1 before.
>
> These parameters depend upon the force field you are using.  Read about the
> parameter set, as well as modifications that may be made to it.  Studies
> have
> suggested that longer cut-off's should be used with membrane proteins.
>  There is
> no substitute for a thorough literature search before starting a project!
>
> > One last question is how to overcome the lincs warnings in position
> > restraint mdrun.
>
> That will depend upon whether or not your system is properly constructed
> and
> energy-minimized.
>
> -Justin
>
> > Thanks in advance.
> >
> > Thanking you,
> > Pawan
> >
> > On Thu, Mar 19, 2009 at 5:01 PM,
> >
> > Pawan Kumar wrote:
> >  > Hi Xavier sir,
> >  >
> >  > Thanks for your valuable reply.
> >  > How can I refine the non-bonded set-up ?
> >
> > rlist, rcoulomb, rvdw as well as coulombtype.  *Never* use cut-off
> > electrostatics for a membrane system (or really any other, for that
> > matter).
> > Your results will be far less accurate than with PME (this is in the
> > literature).
> >
> >  > And where can I specify the time step to 0.0001 ?
> >
> > dt (read the manual).
> >
> > -Justin
> >
> >  > I am new to gromacs.
> >  > Sorry to ask such questions.
> >  >
> >  > Thanking you,
> >  > Pawan
> >  >
> >  >
> >
> >
> >
> > 
> >
> > ___
> > 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 gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
>
> ___
> gmx-users mailing 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!
>
> End of gmx-users Digest, Vol 59, Issue 137
> **
>
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Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hello Justin Sir,

Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came  like "pressure scaling
more than 1%" and "1-4 interactions" and then it stopped after writing few
pdb files. Then I decreased the dt value still lesser (0.1) and this
time it continued with all the given steps but the lipids' structure were
distorted into small fragments.
The other query I have is what should the optimal value for these parameters
for membrane proteins :  rlist, rcoulomb, and rvdw. I have used the value of
1 before.
One last question is how to overcome the lincs warnings in position
restraint mdrun.
Thanks in advance.

Thanking you,
Pawan

On Thu, Mar 19, 2009 at 5:01 PM,

> Pawan Kumar wrote:
> > Hi Xavier sir,
> >
> > Thanks for your valuable reply.
> > How can I refine the non-bonded set-up ?
>
> rlist, rcoulomb, rvdw as well as coulombtype.  *Never* use cut-off
> electrostatics for a membrane system (or really any other, for that
> matter).
> Your results will be far less accurate than with PME (this is in the
> literature).
>
> > And where can I specify the time step to 0.0001 ?
>
> dt (read the manual).
>
> -Justin
>
> > I am new to gromacs.
> > Sorry to ask such questions.
> >
> > Thanking you,
> > Pawan
> >
> >
>
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[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136

[Pawan Kumar]

Hello Justin Sir,

Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came  like "pressure scaling
more than 1%" and "1-4 interactions" and then it stopped after writing few
pdb files. Then I decreased the dt value still lesser (0.1) and this
time it continued with all the given steps but the lipids' structure were
distorted into small fragments.
The other query I have is what should the optimal value for these parameters
for membrane proteins :  rlist, rcoulomb, and rvdw. I have used the value of
1 before.
One last question is how to overcome the lincs warnings in position
restraint mdrun.
Thanks in advance.

Thanking you,
Pawan

On Thu, Mar 19, 2009 at 5:01 PM,

> Pawan Kumar wrote:
> > Hi Xavier sir,
> >
> > Thanks for your valuable reply.
> > How can I refine the non-bonded set-up ?
>
> rlist, rcoulomb, rvdw as well as coulombtype.  *Never* use cut-off
> electrostatics for a membrane system (or really any other, for that
> matter).
> Your results will be far less accurate than with PME (this is in the
> literature).
>
> > And where can I specify the time step to 0.0001 ?
>
> dt (read the manual).
>
> -Justin
>
> > I am new to gromacs.
> > Sorry to ask such questions.
> >
> > Thanking you,
> > Pawan
> >
> >
>
___
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Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hi Xavier sir,

Thanks for your valuable reply.
How can I refine the non-bonded set-up ?
And where can I specify the time step to 0.0001 ?
I am new to gromacs.
Sorry to ask such questions.

Thanking you,
Pawan


On Thu, Mar 19, 2009 at 2:54 PM,  wrote:

> Send gmx-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
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>
> Today's Topics:
>
>   1. Doubt regarding membrane protein in POPC bilayer (Pawan Kumar)
>   2. how to get the the force plot after pulling dynamic
>  simulation using GMX-3.3 (huifang liu)
>   3. Re: Doubt regarding membrane protein in POPC bilayer
>  (XAvier Periole)
>   4. RE: compressibility tensor components,pressurecoupling
>  anisotropic PR, triclinic systems (Berk Hess)
>
>
> ------
>
> Message: 1
> Date: Thu, 19 Mar 2009 10:44:44 +0530
> From: Pawan Kumar 
> Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
> To: gmx-users@gromacs.org
> Message-ID:
><143b0c640903182214n2a603f97q478bfac66f502...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx-users,
>
> Greetings from Pawan.
> I have modelled the structure of a protein using Modeller and then energy
> minimized using gromacs.
> Then I used the popc128a bilayer from Tieleman sir's website for inserting
> the protein.
> I created a bigger bilayer using the genconf command in gromacs.
> I was able to minimize the bigger bilayer and then inserted my protein in
> the bilayer using the genbox command in gromacs.
> I was able to minimize the system.
> But when I tried to do an mdrun for few steps restraining the protein I
> ended with errors like :
> 1) pressure scaling more than 1%
> 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger
> than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation.
> 3) too many lincs warnings.
> 4) Number of grid cells is zero. probably the system and the box collapsed.
>
> I tried to solve these errors by increasing the tau_p value for pressure
> scaling error and higher table-extension value for the 1-4 interaction
> warning in the mdp file but nothing is working out.
> I have given the mdp files at the end for reference.
> Please give me some suggestions as how to continue further.
>
> For energy minimization:
> 
> title   =  Protein in POPC bilayer
> cpp =  /usr/bin/cpp
> define  =  -DFLEXIBLE
> integrator  =  steep
> nsteps  =  5
>
> ; Constrain control
> constraints =  none
>
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout =  100
> nstvout =  100
> nstfout =  100
>
> ; nblist update frequency
> nstlist =  10
>
> ; ns algorithm
> ns_type =  grid
> rlist   =  1
>
> ; Method for doing VdW
> vdw-type=  Cut-off
> rvdw=  1
>
> ; Method for doing electrostatics
> coulombtype=  Cut-off
> rcoulomb=  1
>
> ; Center of mass control
> nstcomm  =  1
>
> ; Periodic boundary conditions
> pbc  =  xyz
>
> ; Mode for center of mass motion removal
> comm-mode=  Linear
>
> ;   Energy minimizing stuff
> emtol=  2250
> emstep   =  0.001
>
>
> For mdrun using position restraints:
> ---
> title   =  Protein in POPC
> cpp =  /usr/bin/cpp
> constraints =  all-bonds
> integrator  =  md
> dt  =  0.002; ps !
> nsteps  =  5000; total 10 ps.
> nstcomm =  1
> nstxout =  50
> nstvout =  1000
> nstfout =  0
> nstlog  =  10
> nstenergy   =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1.0
> rcoulomb=  1.0
> rvdw=  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl  =  berend

[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Dear gmx-users,

Greetings from Pawan.
I have modelled the structure of a protein using Modeller and then energy
minimized using gromacs.
Then I used the popc128a bilayer from Tieleman sir's website for inserting
the protein.
I created a bigger bilayer using the genconf command in gromacs.
I was able to minimize the bigger bilayer and then inserted my protein in
the bilayer using the genbox command in gromacs.
I was able to minimize the system.
But when I tried to do an mdrun for few steps restraining the protein I
ended with errors like :
1) pressure scaling more than 1%
2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation.
3) too many lincs warnings.
4) Number of grid cells is zero. probably the system and the box collapsed.

I tried to solve these errors by increasing the tau_p value for pressure
scaling error and higher table-extension value for the 1-4 interaction
warning in the mdp file but nothing is working out.
I have given the mdp files at the end for reference.
Please give me some suggestions as how to continue further.

For energy minimization:

title   =  Protein in POPC bilayer
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
integrator  =  steep
nsteps  =  5

; Constrain control
constraints =  none

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout =  100
nstvout =  100
nstfout =  100

; nblist update frequency
nstlist =  10

; ns algorithm
ns_type =  grid
rlist   =  1

; Method for doing VdW
vdw-type=  Cut-off
rvdw=  1

; Method for doing electrostatics
coulombtype=  Cut-off
rcoulomb=  1

; Center of mass control
nstcomm  =  1

; Periodic boundary conditions
pbc  =  xyz

; Mode for center of mass motion removal
comm-mode=  Linear

;   Energy minimizing stuff
emtol=  2250
emstep   =  0.001


For mdrun using position restraints:
---
title   =  Protein in POPC
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000; total 10 ps.
nstcomm =  1
nstxout =  50
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps=  ProteinNon-Protein
tau_t   =  0.10.1
ref_t   =  300300
; Energy monitoring
energygrps=  ProteinNon-Protein
; Pressure coupling is not on
Pcoupl  =  berendsen
tau_p   =  5.0 5.0
compressibility =  4.5e-5 4.5e-5
ref_p   =  1.0 1.0
Pcoupl_type =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

Thanking you,

Yours sincerely,
Pawan
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