Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Mark Abraham]

Bing Bing wrote:

Hi!
Thanks for your suggestion on the tutorial. I will try it out.
I actually tried to use the starting structure without going through 
editconf and alteration but it failed. Here's the error:
ERROR: The cut-off length is longer than half the shortest box vector or 
longer than the smallest box diagonal element. Increase the box size or 
decrease rlist.

I've tried on reducing the rlist but still failed. Please advice.


There's a reason for the editconf step. The size of the box is encoded 
in the coordinate file, and needs to be large enough both for your 
system and your model physics. You should not be meddling with your 
model physics (i.e. rlist) unless you know what you're doing :-)


According to the tutorial you suggested, we are suppose to use genbox to 
solvate the membrane and remove those water manually by script that go 
inside the membrane. Does this mean that I'm suppose to throw away the 
water from the starting structure and resolvate it again?


Probably. Water is the easiest thing to generate, so it's the easiest 
thing to remove to simplify things.


Mark
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Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Bing Bing]

Hi!
Thanks for your suggestion on the tutorial. I will try it out.
I actually tried to use the starting structure without going through
editconf and alteration but it failed. Here's the error:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
I've tried on reducing the rlist but still failed. Please advice.

According to the tutorial you suggested, we are suppose to use genbox to
solvate the membrane and remove those water manually by script that go
inside the membrane. Does this mean that I'm suppose to throw away the water
from the starting structure and resolvate it again?

thanks again.

regards,
Bing

On Tue, Jun 23, 2009 at 11:28 PM, Justin A. Lemkul  wrote:

>
>
> Bing Bing wrote:
>
>> Thanks for reply.
>> I've used editconf to define the box by issuing :-
>> editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
>> Is this the correct way of using editconf?
>>
>
> This would be appropriate for a protein, but not a membrane.  What you're
> doing is defining a layer of nothingness around the membrane/water system,
> which may have molecules split across periodic boundaries.  This could be
> the reason everything is blowing up.
>
> Try running EM on the original, unaltered POPC from Tieleman's site.
>
>  And with this i proceed with grompp with the mdp file from previous email
>> followed by mdrun
>>
>> Actually the restraint is require in another system (membrane+protein), i
>> wanted to test it out in the this smaller systme before using it in the
>> complete systme.However, it failed.
>>
>>
> Applying position restraints to every atom of a lipid in the presence of a
> protein still serves little purpose.  If you were to attempt to
> energy-minimize such a system, the clashes (if any) between the protein and
> lipids would go unresolved.  Certainly equilibrating with such restraints
> would be meaningless, as well.
>
> If you're interested, hopefully the tutorial here will help:
>
> http://oldwiki.gromacs.org/index.php/Membrane_Simulations
>
> It is designed for membrane protein simulations.
>
> -Justin
>
>  Thanks in advance
>>
>> regards,
>> bing
>>
>>
>> On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Bing Bing wrote:
>>
>>Hi Justin,
>>I've tried with no restraint and the minimization stopped at the
>>same time. I actually suspect that the restraint is not working
>>at all. My top file is as below:-
>>#include "ffG53a6_lipid.itp"
>>#include "popc.itp"
>>#ifdef POSRES
>>#include "posres_popc.itp"
>>#endif
>>#ifdef FLEX_SPC
>>#include "flexspc.itp"
>>#else
>>#include "spc.itp"
>>#endif
>>
>>[ system ]
>>; name
>>Pure POPC bilayer with 128 lipids 2460 water
>>
>>[ molecules ]
>>; name  number
>>POPC128
>>SOL2460
>>
>>my posres_popc.itp is as below:-
>>[ position_restraints ]
>>; atom  type  fx  fy  fz
>>1 1  1000  1000  1000
>>.
>>   51 1  1000  1000  1000
>>   52 1  1000  1000  1000
>>
>>my mdp file as below :-
>>define = -DPOSRES
>>integrator = steep
>>emtol = 1000
>>emstep = 0.01
>>nsteps = 100
>>rlist = 1.2
>>coulombtype = PME
>>rcoulomb = 1.2
>>rvdw = 1.2
>>constraints = none
>>
>>May i know that is the top, posres and also the mdp file
>>correctly done?
>>
>>
>>Well, they are syntactically correct, it seems.  I see no purpose in
>>restraining lipids during a minimization, however.
>>
>>
>>And by looking at the log file in the previous mail, is it
>>confirm that it manage to read the restraint file?
>>
>>
>>Can't tell.  Your system is crashing instantly for some reason.
>>
>>
>>The starting structure is taken from Peter Tielemen website and
>>what i did is editconf to make box and i didn't solvate because
>>the starting structure come together with water. I'm not sure
>>this is the correct way of doing it. Please advice.
>>
>>
>>Please define "editconf to make box" - have you somehow manipulated
>>the structure?  That could be a source of error.  The structure that
>>Tieleman provides minimized for me with no problem when I used it
>>recently.
>>
>>-Justin
>>
>>
>>
>>Thanks in advance.
>>Bing
>>
>>
>>
>>On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Bing Bing wrote:
>>
>>   Hi! I'm a postgraduate student from Malaysia and currently
>>   facing energy minimization problem for my membrane system.
>>   I'm trying to

Re: 回复：[gmx-users] Re: How to freeze the atoms ?

[Vitaly V. Chaban]

I do not know such effect although work with the 'freeze' option for a
number of years in many gromacs versions.

Are you sure that the numbers of the atoms in your ndx file are the same as
in the corresponding residues? I suggest that you should look for a problem
there.

Do the atoms move only when EM is performed or during MD run as well?

- Vitaly


2009/6/24 

> Dear all
>
>The CNT itself does not move. Only C and O in carbonyl groups move
> and the distance of movement is not large. As I wrote, Each carbonyl group
> (C and O ) is considered as a residue named "Car" and the group name of
> carbonyl in the ndx file is "Car", too. Is there anything wrong with the
> groups?
>
>Is it possible that the frozen atoms move a short distance due to
> the strong electrostatic forces. C in the CNT has no charge, while atoms in
> carbonyl groups take charges.
>
>Thank you for your time!
>
>
> - 原始邮件 -
> 发件人：Vitaly V. Chaban 
> 收件人：gmx-us...@gromacs.org
> 主题：[gmx-users] Re: How to freeze the atoms?
> 日期：2009-6-23 18:04:35
>
> >
> > Dear all
> >I attach 8 carbonyl groups onto a
> > carbon nanotube (CNT). Each carbonyl group is considered as a residue
> named
> > "Car" and each carbon atom in the CNT is considered as a residue named
> > "Gr1". In the mdp file, the freezegrps are Gr1 and Car, and the freezedim
> > are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in
> the
> > carbonyl groups are fixed in three dimensions and they can not move in
> any
> > direction. However, when I made the energy minimization, the coordinates
> of
> > C and O in carbonyl groups changed.
> >   How can I really fix the atoms? Look forward
> > for your suggestions!
> >
>
> All the atoms which relate to your frozen groups should be non-movable
> during MD.
>
> >the coordinates of C and O in carbonyl groups changed.
>
> Only ones of CHO changed? And the CNT itself is nonmovable? Check your
> groups please.
>


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
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Re: [gmx-users] WARNING: negative index -1 in group System

[Justin A. Lemkul]

Christopher Rowan wrote:

Hi,

Allow me to be the first to archive a message with "negative index".

I ask for an index file:
make_ndx_s -f ???.pdb -o ???.ndx
and specify:
a AG
to select all the silver atoms into a group.
The index file then clearly numbers and lists the atoms: all in [
system ], again all atom numbers in empty brackets [   ] and then my
silver atoms in the [ AG ] group.


First, it would be helpful to know which version of Gromacs you're using, 
especially if this is a bug in an older version.  If it is the most current 
version (4.0.5), it is of much greater interest :)


What I don't understand is why you have a group with no name; that shouldn't be. 
 If you're defining AG atoms, then you should have [ System ] and [ AG ].



I proceed to define a box:
editconf_s -f ???.pdb  -n ???.ndx -o ???.gro -bt cubic

The output gives:

...
Select a group for output:

WARNING: negative index -1 in group System



I'm assuming you've check the entire [ System ] directive to ensure that all 
indices are positive?  With the generation of a "no-name" group, it is possible 
that something funky is going on.




WARNING: negative index -1 in group System

Group 0 (  System) has68 elements
Group 1 (  AG) has13 elements
Select a group: 0
Selected 0: 'System'
Segmentation fault



Does the command work without the index file?  If you're specifying a box to 
contain the entire system, then you shouldn't need the index file.


-Justin


Perplexing.

I found Travis Trudeau's message about having a zero index and tried
finding atom numbering:
grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx

But again got:

...
initialising group options...
processing index file...

WARNING: negative index -1 in group System


WARNING: negative index -1 in group System

Making dummy/rest group for T-Coupling containing 33 elements
...

So, if anyone could shed some light on how to overcome the negative
index hurdle it would be much appreciated,
Chris Rowan
University of Victoria
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--


Justin A. Lemkul
Ph.D. Candidate
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] Re: WARNING: negative index -1 in group System

[Christopher Rowan]

Sorry to post again,

But I meant to say that for atom indexing I looked using gmxdump:

gmxdump_s -s ???.tpr -f ???.pdb -nr

and found only indexing starting at zero; e.g

atom[0]={name="AG"}

Cheers,
Chris Rowan
University of Victoria





2009/6/23 Christopher Rowan :
> Hi,
>
> Allow me to be the first to archive a message with "negative index".
>
> I ask for an index file:
> make_ndx_s -f ???.pdb -o ???.ndx
> and specify:
> a AG
> to select all the silver atoms into a group.
> The index file then clearly numbers and lists the atoms: all in [
> system ], again all atom numbers in empty brackets [   ] and then my
> silver atoms in the [ AG ] group.
> I proceed to define a box:
> editconf_s -f ???.pdb  -n ???.ndx -o ???.gro -bt cubic
>
> The output gives:
>
> ...
> Select a group for output:
>
> WARNING: negative index -1 in group System
>
>
> WARNING: negative index -1 in group System
>
> Group 0 (  System) has68 elements
> Group 1 (  AG) has13 elements
> Select a group: 0
> Selected 0: 'System'
> Segmentation fault
>
> Perplexing.
>
> I found Travis Trudeau's message about having a zero index and tried
> finding atom numbering:
> grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx
>
> But again got:
>
> ...
> initialising group options...
> processing index file...
>
> WARNING: negative index -1 in group System
>
>
> WARNING: negative index -1 in group System
>
> Making dummy/rest group for T-Coupling containing 33 elements
> ...
>
> So, if anyone could shed some light on how to overcome the negative
> index hurdle it would be much appreciated,
> Chris Rowan
> University of Victoria
>
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[gmx-users] WARNING: negative index -1 in group System

[Christopher Rowan]

Hi,

Allow me to be the first to archive a message with "negative index".

I ask for an index file:
make_ndx_s -f ???.pdb -o ???.ndx
and specify:
a AG
to select all the silver atoms into a group.
The index file then clearly numbers and lists the atoms: all in [
system ], again all atom numbers in empty brackets [   ] and then my
silver atoms in the [ AG ] group.
I proceed to define a box:
editconf_s -f ???.pdb  -n ???.ndx -o ???.gro -bt cubic

The output gives:

...
Select a group for output:

WARNING: negative index -1 in group System


WARNING: negative index -1 in group System

Group 0 (  System) has68 elements
Group 1 (  AG) has13 elements
Select a group: 0
Selected 0: 'System'
Segmentation fault

Perplexing.

I found Travis Trudeau's message about having a zero index and tried
finding atom numbering:
grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx

But again got:

...
initialising group options...
processing index file...

WARNING: negative index -1 in group System


WARNING: negative index -1 in group System

Making dummy/rest group for T-Coupling containing 33 elements
...

So, if anyone could shed some light on how to overcome the negative
index hurdle it would be much appreciated,
Chris Rowan
University of Victoria
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Re: [gmx-users] mdrun -c option "did not work"

[David van der Spoel]

Jérôme Baffreau wrote:

Hello everyone,
 
this is my very first post on GROMACS mailing list, so please apologize 
if my question seems very simple.
 
Here is my problem... I ran a calculation using GROMACS 4.0.3 and this 
command line:
 
mpirun -np 32 mdrun -s prot_md.tpr -c prot_md.gro -g md.log -e md.edr -o 
prot_md.trr -deffnm md -nov
 
I think everything went well, but the prot_md.gro (final structure) file 
has NOT been generated so I'm wondering if there's a way to generate it 
from tpr, trr ou xct output files?


Yes, use trjconv.

Did your run finish normally otherwise? Check your md.log, it should 
have performance statistics at the bottom of the file. You should also 
consider upgrading to 4.0.5, in particular if the problem does not go 
away...
 
Thanks a lot,
 
Jerome B.
 
**

Jerome Baffreau, PhD
Stagiaire postdoctoral - Postdoctoral fellow
Departement de Biochimie - Biochemistry Department
Universite de Montreal
Montreal, QC
Canada




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David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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[gmx-users] mdrun -c option "did not work"

[Jérôme Baffreau]

Hello everyone,

this is my very first post on GROMACS mailing list, so please apologize if my 
question seems very simple.

Here is my problem... I ran a calculation using GROMACS 4.0.3 and this command 
line:

mpirun -np 32 mdrun -s prot_md.tpr -c prot_md.gro -g md.log -e md.edr -o 
prot_md.trr -deffnm md -nov

I think everything went well, but the prot_md.gro (final structure) file has 
NOT been generated so I'm wondering if there's a way to generate it from tpr, 
trr ou xct output files?

Thanks a lot,

Jerome B.

**
Jerome Baffreau, PhD
Stagiaire postdoctoral - Postdoctoral fellow
Departement de Biochimie - Biochemistry Department
Universite de Montreal
Montreal, QC
Canada
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Re: [gmx-users] impose a external magnetic field

[David van der Spoel]

风 大 wrote:

Dear all,


I want to impose a homogeneous static magnetic field on a solution. I 
just wonder if the gromacs can do it, anyway? I believe gromacs can. 
However, could anyone give me some suggestions to do it?

This is not implemented. I assume you would want to add a Lorentz force?
The best way to add this code is in the subroutine that does the 
electric field stuff (src/mdlib/sim_util.c, routine calc_f_el).



Thanks a lot!



好玩贺卡等你发，邮箱贺卡全新上线！ 
 






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David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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[gmx-users] impose a external magnetic field

[风 大]

Dear all,


I want to impose a homogeneous static magnetic field on a solution. I just 
wonder if the gromacs can do it, anyway? I believe gromacs can. However, could 
anyone give me some suggestions to do it?


Thanks a lot!




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Re: [gmx-users] parallel processing using LAN

[Mark Abraham]

akalabya bissoyi wrote:
For parallel processing is it possible to use the system connected to 
the local area network something like clustering the system for simulation.

plz suggest me so that i can use my resources for faster simulation.


Yes it's possible, but you will not scale to more than a handful of 
processors unless your network connections are very good. Gigabit 
ethernet is not very good.


Mark
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Re: [gmx-users] simulation of protein in presence of ATP

[Mark Abraham]

nikhil damle wrote:
OK till here done ! the pdb file generated for EM should have ATP 
molecule @proper position as input .top file has the ATP.itp included. 
It did not have. If I do -ci it would randomly replace the solvent. I 
want ATP @ its proper location. how do i do this ?


Like I implied several emails ago, you should order the [molecules] 
entries according to the coordinate file, as normal.


Mark
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Re: [gmx-users] simulation of protein in presence of ATP

[Justin A. Lemkul]

nikhil damle wrote:
OK till here done ! the pdb file generated for EM should have ATP 
molecule @proper position as input .top file has the ATP.itp included. 
It did not have. If I do -ci it would randomly replace the solvent. I 
want ATP @ its proper location. how do i do this ?


http://oldwiki.gromacs.org/index.php/Tutorials#General

The "drug-enzyme complex" tutorial will tell you how to do this.  You won't need 
to use PRODRG, as the tutorial does, since you have already generated your 
topologies with pdb2gmx.  But everything else is still applicable.


-Justin




*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Tuesday, 23 June, 2009 4:41:22 PM
*Subject:* Re: [gmx-users] simulation of protein in presence of ATP



nikhil damle wrote:
 > Thanks a lot for kind help. I reached till grompp before minimizing 
energy of the system where I received an error msg as "Invalid order for 
directive defaults: filename; line x" !!! what is 
the meaning of this error ? Is it something to do with path variable 
problem or writing things in improper order ?

 >

Probably, if you've processed your protein with pdb2gmx as well as the 
ATP molecule, you have two .top files, each of which contains an 
#include statement for your force field, so you're duplicating these 
entries.


Without any information about the contents of your .top(s) or how you've 
actually built things, this is just a guess.


See here:

http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

-Justin

 > Nikhil
 >
 > 
 > *From:* Mark Abraham >
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Tuesday, 23 June, 2009 12:35:12 PM
 > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
 >
 > nikhil damle wrote:
 >  > Hi,
 >  >  We can use max 4 coloumns for naming atoms. But .rtp file has 
5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But 
now the error is "atom N not found in residue 1ATP while combining tdb 
and rtp"

 >
 > pdb2gmx tries to cap termini of peptides automatically, but this 
isn't a peptide. So look at pdb2gmx -h and choose the option that will 
allow you to interactively choose that no terminal capping needs to take 
place.

 >
 > Mark
 >
 >  > 

 >  > *From:* Mark Abraham  >>
 >  > *To:* Discussion list for GROMACS users  >>

 >  > *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
 >  > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
 >  >
 >  > nikhil damle wrote:
 >  >  > Hi,
 >  >  >
 >  >  >Thanks a lot for the reply. I am submitting ATP crds as 
ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file 
ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. 
Please find ATP.pdb file attached herewith.

 >  >
 >  > You've broken the PDB format, which encodes the information in 
fixed-column style. See 
http://www.wwpdb.org/documentation/format32/v3.2.html

 >  >
 >  > Mark
 >  > ___
 >  > gmx-users mailing listgmx-users@gromacs.org 
 >  >>

 >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
 >  > Please search the archive at http://www.gromacs.org/search before 
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 >

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 >  > Ple

Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Justin A. Lemkul]

Bing Bing wrote:

Thanks for reply.
I've used editconf to define the box by issuing :-
editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
Is this the correct way of using editconf?


This would be appropriate for a protein, but not a membrane.  What you're doing 
is defining a layer of nothingness around the membrane/water system, which may 
have molecules split across periodic boundaries.  This could be the reason 
everything is blowing up.


Try running EM on the original, unaltered POPC from Tieleman's site.

And with this i proceed with grompp with the mdp file from previous 
email followed by mdrun


Actually the restraint is require in another system (membrane+protein), 
i wanted to test it out in the this smaller systme before using it in 
the complete systme.However, it failed.




Applying position restraints to every atom of a lipid in the presence of a 
protein still serves little purpose.  If you were to attempt to energy-minimize 
such a system, the clashes (if any) between the protein and lipids would go 
unresolved.  Certainly equilibrating with such restraints would be meaningless, 
as well.


If you're interested, hopefully the tutorial here will help:

http://oldwiki.gromacs.org/index.php/Membrane_Simulations

It is designed for membrane protein simulations.

-Justin


Thanks in advance

regards,
bing


On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul > wrote:




Bing Bing wrote:

Hi Justin,
I've tried with no restraint and the minimization stopped at the
same time. I actually suspect that the restraint is not working
at all. My top file is as below:-
#include "ffG53a6_lipid.itp"
#include "popc.itp"
#ifdef POSRES
#include "posres_popc.itp"
#endif
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Pure POPC bilayer with 128 lipids 2460 water

[ molecules ]
; name  number
POPC128
SOL2460

my posres_popc.itp is as below:-
[ position_restraints ]
; atom  type  fx  fy  fz
1 1  1000  1000  1000
.
   51 1  1000  1000  1000
   52 1  1000  1000  1000

my mdp file as below :-
define = -DPOSRES
integrator = steep
emtol = 1000
emstep = 0.01
nsteps = 100
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
constraints = none

May i know that is the top, posres and also the mdp file
correctly done?


Well, they are syntactically correct, it seems.  I see no purpose in
restraining lipids during a minimization, however.


And by looking at the log file in the previous mail, is it
confirm that it manage to read the restraint file?


Can't tell.  Your system is crashing instantly for some reason.


The starting structure is taken from Peter Tielemen website and
what i did is editconf to make box and i didn't solvate because
the starting structure come together with water. I'm not sure
this is the correct way of doing it. Please advice.


Please define "editconf to make box" - have you somehow manipulated
the structure?  That could be a source of error.  The structure that
Tieleman provides minimized for me with no problem when I used it
recently.

-Justin



Thanks in advance.
Bing



On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Bing Bing wrote:

   Hi! I'm a postgraduate student from Malaysia and currently
   facing energy minimization problem for my membrane system.
   I'm trying to perform energy minimization for an empty POPC
   membrane with position restraint on the lipid.
Minimization stop
   due to inf Fmax. And I noticed that in the log file as
below:-
 Initiating Steepest Descents
   Max number of connections per atom is 25
   Total number of connections is 84976
   Max number of graph edges per atom is 4
   Total number of graph edges is 22896
   Going to use C-settle (2460 waters)
   wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra =
0.0384897
   rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH
= 0.1
   Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
   Steepest Descents:
 Tolerance (Fmax)   =  1.0e+03
 Number of steps=  100
   Grid: 11 x 11 x 11 cells
 Step   Time Lambda
  

RE: [gmx-users] pullx.xvg Meaning of output?

[Berk Hess]

Hi,

Everything depends on what you want to accomplish, which you
do not write.
I don't see why you would want to look at single atoms.
Since you pull on COM's, only the COM coordinates are relevant.
If you want to look at single atoms, simply store them in the xtc file.

If you have only two groups, there is no physical difference between
the reference group and  the first pull group. They are simply two
groups between which the distance is calculated and the forces act.
If you used an absolute reference, 0Z is the absolute reference coordinate,
not the coordinate of a group.

Berk

> Date: Tue, 23 Jun 2009 14:39:48 +0200
> From: ilona.bal...@bioquant.uni-heidelberg.de
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> 
> 
> Dear Berk,
> 
> Thanks for the quick reply. That leads me to my next questions:
> *I used the whole N and C residues for pulling. Is there any way of  
> reconstructing the values for the single atoms? Or do you recommend  
> only to pull N and C in the first place?
> *What does the reference group actually do? Can I simply leave it out?  
> Does it influence pulling?  What would be a good reference group? A  
> random backbone atom from the middle of the protein?
> 
> I'm looking forward to your reply. Thank you very much in advance.
> 
> Best wishes, Ilona
> 
> 
> Quoting Berk Hess :
> 
> >
> > Hi,
> >
> > This is actually not (yet) documented.
> > 0Z is the Z-coordinate of group 0.
> > 1dZ is the the Z-coordinate of group 1 minus the one of group 0.
> >
> > Berk
> >
> >> Date: Tue, 23 Jun 2009 12:54:37 +0200
> >> From: ilona.bal...@bioquant.uni-heidelberg.de
> >> To: gmx-users@gromacs.org
> >> Subject: [gmx-users] pullx.xvg  Meaning of output?
> >>
> >> Hi!
> >>
> >> I am trying to understand the output of my pulling simulation:
> >> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and
> >> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.
> >> Since the website is down I cannot check on previous issues, so sorry
> >> for asking the same question again as I already asked last week but
> >> which remained unanswered.
> >>
> >> I would appreciate any advice.
> >>
> >> Thanks a lot. Ilona
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
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> 
> 
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> INF 276
> 69120 Heidelberg
> Tel.: 06221-5451268
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Re: [gmx-users] simulation of protein in presence of ATP

[nikhil damle]

OK till here done ! the pdb file generated for EM should have ATP molecule 
@proper position as input .top file has the ATP.itp included. It did not have. 
If I do -ci it would randomly replace the solvent. I want ATP @ its proper 
location. how do i do this ?





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Tuesday, 23 June, 2009 4:41:22 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP



nikhil damle wrote:
> Thanks a lot for kind help. I reached till grompp before minimizing energy of 
> the system where I received an error msg as "Invalid order for directive 
> defaults: filename; line x" !!! what is the meaning of 
> this error ? Is it something to do with path variable problem or writing 
> things in improper order ?
> 

Probably, if you've processed your protein with pdb2gmx as well as the ATP 
molecule, you have two .top files, each of which contains an #include statement 
for your force field, so you're duplicating these entries.

Without any information about the contents of your .top(s) or how you've 
actually built things, this is just a guess.

See here:

http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

-Justin

> Nikhil
> 
> 
> *From:* Mark Abraham 
> *To:* Discussion list for GROMACS users 
> *Sent:* Tuesday, 23 June, 2009 12:35:12 PM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
> 
> nikhil damle wrote:
>  > Hi,
>  >  We can use max 4 coloumns for naming atoms. But .rtp file has 5 
> coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the 
> error is "atom N not found in residue 1ATP while combining tdb and rtp"
> 
> pdb2gmx tries to cap termini of peptides automatically, but this isn't a 
> peptide. So look at pdb2gmx -h and choose the option that will allow you to 
> interactively choose that no terminal capping needs to take place.
> 
> Mark
> 
>  > 
>  > *From:* Mark Abraham  >
>  > *To:* Discussion list for GROMACS users  >
>  > *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
>  > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
>  >
>  > nikhil damle wrote:
>  >  > Hi,
>  >  >
>  >  >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to 
> pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I 
> converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb 
> file attached herewith.
>  >
>  > You've broken the PDB format, which encodes the information in 
> fixed-column style. See http://www.wwpdb.org/documentation/format32/v3.2.html
>  >
>  > Mark
>  > ___
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Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Bing Bing]

Thanks for reply.
I've used editconf to define the box by issuing :-
editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
Is this the correct way of using editconf?
And with this i proceed with grompp with the mdp file from previous email
followed by mdrun

Actually the restraint is require in another system (membrane+protein), i
wanted to test it out in the this smaller systme before using it in the
complete systme.However, it failed.

Thanks in advance

regards,
bing


On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul  wrote:

>
>
> Bing Bing wrote:
>
>> Hi Justin,
>> I've tried with no restraint and the minimization stopped at the same
>> time. I actually suspect that the restraint is not working at all. My top
>> file is as below:-
>> #include "ffG53a6_lipid.itp"
>> #include "popc.itp"
>> #ifdef POSRES
>> #include "posres_popc.itp"
>> #endif
>> #ifdef FLEX_SPC
>> #include "flexspc.itp"
>> #else
>> #include "spc.itp"
>> #endif
>>
>> [ system ]
>> ; name
>> Pure POPC bilayer with 128 lipids 2460 water
>>
>> [ molecules ]
>> ; name  number
>> POPC128
>> SOL2460
>>
>> my posres_popc.itp is as below:-
>> [ position_restraints ]
>> ; atom  type  fx  fy  fz
>> 1 1  1000  1000  1000
>> .
>>51 1  1000  1000  1000
>>52 1  1000  1000  1000
>>
>> my mdp file as below :-
>> define = -DPOSRES
>> integrator = steep
>> emtol = 1000
>> emstep = 0.01
>> nsteps = 100
>> rlist = 1.2
>> coulombtype = PME
>> rcoulomb = 1.2
>> rvdw = 1.2
>> constraints = none
>>
>> May i know that is the top, posres and also the mdp file correctly done?
>>
>
> Well, they are syntactically correct, it seems.  I see no purpose in
> restraining lipids during a minimization, however.
>
>  And by looking at the log file in the previous mail, is it confirm that it
>> manage to read the restraint file?
>>
>
> Can't tell.  Your system is crashing instantly for some reason.
>
>  The starting structure is taken from Peter Tielemen website and what i did
>> is editconf to make box and i didn't solvate because the starting structure
>> come together with water. I'm not sure this is the correct way of doing it.
>> Please advice.
>>
>
> Please define "editconf to make box" - have you somehow manipulated the
> structure?  That could be a source of error.  The structure that Tieleman
> provides minimized for me with no problem when I used it recently.
>
> -Justin
>
>
>>
>> Thanks in advance.
>> Bing
>>
>>
>>
>> On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Bing Bing wrote:
>>
>>Hi! I'm a postgraduate student from Malaysia and currently
>>facing energy minimization problem for my membrane system.
>>I'm trying to perform energy minimization for an empty POPC
>>membrane with position restraint on the lipid. Minimization stop
>>due to inf Fmax. And I noticed that in the log file as below:-
>>  Initiating Steepest Descents
>>Max number of connections per atom is 25
>>Total number of connections is 84976
>>Max number of graph edges per atom is 4
>>Total number of graph edges is 22896
>>Going to use C-settle (2460 waters)
>>wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
>>rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
>>Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
>>Steepest Descents:
>>  Tolerance (Fmax)   =  1.0e+03
>>  Number of steps=  100
>>Grid: 11 x 11 x 11 cells
>>  Step   Time Lambda
>> 00.00.0
>>  Energies (kJ/mol)
>>  Bond  AngleProper Dih. Ryckaert-Bell.
>> Improper Dih.
>>   1.64082e+051.71875e+044.06560e+036.45104e+03
>>   8.36392e+03
>> LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)
>>  Coul. recip.
>>  2.12067e-314   2.12067e-314   -1.58963e+04   -1.05392e+05
>>  -1.15292e+05
>> Position Rest.  Potential Pressure (bar)
>>   0.0e+00   -3.64297e+04nan
>>
>>
>> >From the looks of some of these energies (i.e., LJ-14,
>>Coulomb-14), it looks like something is severely wrong with your
>>starting structure, and applying position restraints probably isn't
>>helping.
>>
>>Try the minimization without restraints and see if it works.
>>
>>Also, have you set the appropriate "define" line in the .mdp file,
>>corresponding to what is prescribed in the .top?
>>
>>-Justin
>>
>>---
>>Program mdrun_d, VERSION 4.0.5
>>Source code file: nsgrid.c, line: 357
>>Range checking error:
>>Explanation: During neighborsearching, we assign each particle
>>to a grid
>>based on its coordinates. If your system contains collisions or

Re: [gmx-users] genbox error at futil.c

[Justin A. Lemkul]

iulek wrote:

   Thanks for replying.

   Humm..., maybe I see now. As a beginner I intended to keep all files 
produced and better inspect what happens in sequence, but I did not want 
to use the conventional renaming. But it seems that for the topology 
file, the common procedure is to keep always one only name through the 
several steps, right? That is what I understand with




You can keep the same name, or manually make your own backup copies along the 
way (topol_orig.top, topol_after_sol.top, etc).



"
Option Filename  Type Description

 -p  topol.top  In/Out, Opt. Topology file
"

   so, the same name for input and output, yet genbox renames the old 
one according to the conventions (which in my script I could then 
further "re-rename").


Right, genbox will not make a new file for you, it simply processes the input 
topology, which becomes the output once it is modified.


-Justin

   And... genbox does need a previous topology file (RecA_nat_b4em.top 
was intended to be the output file!).

   Thanks, again.

Jorge




iulek wrote:

Hi!

I am a very beginner, trying to make some dynamics of a protein 
in a water box, after doing some (web) tutorials. I googled first for 
this (possibly simple) error, found one reference, but cannot see it, 
possibly because the gromacs site is under changes.

I ran pdb2gmx and editconf. Then at genbox I get the error:

"
Processing topology

---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330

File input/output error:
RecA_nat_b4em.top
---
"
 


So is the topology in the current working directory?

-Justin



The command line is:
 > genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o 
${MOL}_b4em.gro << eof > genbox.log

eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,

Jorge




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--


Justin A. Lemkul
Ph.D. Candidate
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] Problem in energy minimization for a empty membrane system

[Justin A. Lemkul]

Bing Bing wrote:

Hi Justin,
I've tried with no restraint and the minimization stopped at the same 
time. I actually suspect that the restraint is not working at all. My 
top file is as below:-

#include "ffG53a6_lipid.itp"
#include "popc.itp"
#ifdef POSRES
#include "posres_popc.itp"
#endif
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Pure POPC bilayer with 128 lipids 2460 water

[ molecules ]
; name  number
POPC128
SOL2460

my posres_popc.itp is as below:-
[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  1000  1000  1000
.
51 1  1000  1000  1000
52 1  1000  1000  1000

my mdp file as below :-
define = -DPOSRES
integrator = steep
emtol = 1000
emstep = 0.01
nsteps = 100
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
constraints = none

May i know that is the top, posres and also the mdp file correctly done?


Well, they are syntactically correct, it seems.  I see no purpose in restraining 
lipids during a minimization, however.


And by looking at the log file in the previous mail, is it confirm that 
it manage to read the restraint file?


Can't tell.  Your system is crashing instantly for some reason.

The starting structure is taken from Peter Tielemen website and what i 
did is editconf to make box and i didn't solvate because the starting 
structure come together with water. I'm not sure this is the correct way 
of doing it. Please advice.


Please define "editconf to make box" - have you somehow manipulated the 
structure?  That could be a source of error.  The structure that Tieleman 
provides minimized for me with no problem when I used it recently.


-Justin




Thanks in advance.
Bing


On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul > wrote:




Bing Bing wrote:

Hi! I'm a postgraduate student from Malaysia and currently
facing energy minimization problem for my membrane system.
I'm trying to perform energy minimization for an empty POPC
membrane with position restraint on the lipid. Minimization stop
due to inf Fmax. And I noticed that in the log file as below:-
  Initiating Steepest Descents
Max number of connections per atom is 25
Total number of connections is 84976
Max number of graph edges per atom is 4
Total number of graph edges is 22896
Going to use C-settle (2460 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=  100
Grid: 11 x 11 x 11 cells
  Step   Time Lambda
 00.00.0
  Energies (kJ/mol)
  Bond  AngleProper Dih. Ryckaert-Bell.
 Improper Dih.
   1.64082e+051.71875e+044.06560e+036.45104e+03  
 8.36392e+03
 LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  
Coul. recip.
  2.12067e-314   2.12067e-314   -1.58963e+04   -1.05392e+05  
-1.15292e+05

 Position Rest.  Potential Pressure (bar)
   0.0e+00   -3.64297e+04nan


 >From the looks of some of these energies (i.e., LJ-14,
Coulomb-14), it looks like something is severely wrong with your
starting structure, and applying position restraints probably isn't
helping.

Try the minimization without restraints and see if it works.

Also, have you set the appropriate "define" line in the .mdp file,
corresponding to what is prescribed in the .top?

-Justin

---
Program mdrun_d, VERSION 4.0.5
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle
to a grid
based on its coordinates. If your system contains collisions or
parameter
errors that give particles very high velocities you might end up
with some
coordinates being +-Infinity or NaN (not-a-number). Obviously,
we cannot
put these on a grid, so this is usually where we detect those
errors.
Make sure your system is properly energy-minimized and that the
potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [
0 .. 1331 ]
  the position restraint energy is 0 as highlighted. Here's the
position restraint file :-
 [ position_restraints ]
; atom  type  fx  fy  fz
1 1  1000  1000  5000
5 1  1000  1000  1000
6 1  1000  

Re: [gmx-users] Parameters for -Si-Si- chains?

[Florian Dommert]

* Semen Esilevsky  [2009-06-23 06:06:58 -0700]:



ThanksTsjerk, Google is definitely our best friend :) However, digging for 
parameters and testing the funny mixed force field is not justified in this 
case - the project is small as well as the amount of financing :) So, I whould 
be very grateful if somebody could point me to the ready-to-use -Si-Si- GROMACS 
topologies (if they exists of course).


Mixing force field parameters is very dangerous, because they are
parametrized in respect to each other, therefore I am quite sure that
Tserk did not meant that you should mix any parameters. The choice of a
suitable set of parameters depends on many factors, the environment you
simulate, the boundary conditions, temperature ... . So I interpret
Tsjerks reply in the following way: literature should be searched to find a 
reference
article describing the simulation of a very similar system, from this
reference a consistent force field should derived and applied in your
simulation.

Flo





- Original Message 
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Tuesday, June 23, 2009 11:22:39 AM
Subject: Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:

Dear All,
Our colleges asked me to do some rather simple MD of the organic-silicone
compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
not so simple because of the force field. Does anybody know about parameters
for such systems, which are adapted for GROMACS? I've only found -Si-O-
-parameters in standard ffgmx, which is not what I need. OPLS also has no
parameters for -Si-Si-Si- chains. Probably somebody know about other force
fields from which it is possible to transfer missed parameters?

Regards,
Semen


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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--
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658

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Re: Re: [gmx-users] genbox error at futil.c

[iulek]

   Thanks for replying.

   Humm..., maybe I see now. As a beginner I intended to keep all files 
produced and better inspect what happens in sequence, but I did not want 
to use the conventional renaming. But it seems that for the topology 
file, the common procedure is to keep always one only name through the 
several steps, right? That is what I understand with


"
Option Filename  Type Description

 -p  topol.top  In/Out, Opt. Topology file
"

   so, the same name for input and output, yet genbox renames the old 
one according to the conventions (which in my script I could then 
further "re-rename").
   And... genbox does need a previous topology file (RecA_nat_b4em.top 
was intended to be the output file!).

   Thanks, again.

Jorge




iulek wrote:

Hi!

I am a very beginner, trying to make some dynamics of a protein 
in a water box, after doing some (web) tutorials. I googled first for 
this (possibly simple) error, found one reference, but cannot see it, 
possibly because the gromacs site is under changes.

I ran pdb2gmx and editconf. Then at genbox I get the error:

"
Processing topology

---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330

File input/output error:
RecA_nat_b4em.top
---
"
 


So is the topology in the current working directory?

-Justin



The command line is:
 > genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o 
${MOL}_b4em.gro << eof > genbox.log

eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,

Jorge




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[gmx-users] parallel processing using LAN

[akalabya bissoyi]

For parallel processing is it possible to use the system connected to the
local area network something like clustering the system for simulation.
plz suggest me so that i can use my resources for faster simulation.

thanks

AKALABYA BISSOYI
N.I.T.Rourkela.
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Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Bing Bing]

Hi Justin,
I've tried with no restraint and the minimization stopped at the same time.
I actually suspect that the restraint is not working at all. My top file is
as below:-
#include "ffG53a6_lipid.itp"
#include "popc.itp"
#ifdef POSRES
#include "posres_popc.itp"
#endif
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Pure POPC bilayer with 128 lipids 2460 water

[ molecules ]
; name  number
POPC128
SOL2460

my posres_popc.itp is as below:-
[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  1000  1000  1000
.
51 1  1000  1000  1000
52 1  1000  1000  1000

my mdp file as below :-
define = -DPOSRES
integrator = steep
emtol = 1000
emstep = 0.01
nsteps = 100
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
constraints = none

May i know that is the top, posres and also the mdp file correctly done?
And by looking at the log file in the previous mail, is it confirm that it
manage to read the restraint file?
The starting structure is taken from Peter Tielemen website and what i did
is editconf to make box and i didn't solvate because the starting structure
come together with water. I'm not sure this is the correct way of doing it.
Please advice.


Thanks in advance.
Bing


On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul  wrote:

>
>
> Bing Bing wrote:
>
>> Hi! I'm a postgraduate student from Malaysia and currently facing energy
>> minimization problem for my membrane system.
>> I'm trying to perform energy minimization for an empty POPC membrane with
>> position restraint on the lipid. Minimization stop due to inf Fmax. And I
>> noticed that in the log file as below:-
>>   Initiating Steepest Descents
>> Max number of connections per atom is 25
>> Total number of connections is 84976
>> Max number of graph edges per atom is 4
>> Total number of graph edges is 22896
>> Going to use C-settle (2460 waters)
>> wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
>> rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
>> Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+03
>>   Number of steps=  100
>> Grid: 11 x 11 x 11 cells
>>   Step   Time Lambda
>>  00.00.0
>>   Energies (kJ/mol)
>>   Bond  AngleProper Dih. Ryckaert-Bell.  Improper Dih.
>>1.64082e+051.71875e+044.06560e+036.45104e+038.36392e+03
>>  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.
>>   2.12067e-314   2.12067e-314   -1.58963e+04   -1.05392e+05   -1.15292e+05
>>  Position Rest.  Potential Pressure (bar)
>>0.0e+00   -3.64297e+04nan
>>
>>
> From the looks of some of these energies (i.e., LJ-14, Coulomb-14), it
> looks like something is severely wrong with your starting structure, and
> applying position restraints probably isn't helping.
>
> Try the minimization without restraints and see if it works.
>
> Also, have you set the appropriate "define" line in the .mdp file,
> corresponding to what is prescribed in the .top?
>
> -Justin
>
>  ---
>> Program mdrun_d, VERSION 4.0.5
>> Source code file: nsgrid.c, line: 357
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or parameter
>> errors that give particles very high velocities you might end up with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the potential
>> energy seems reasonable before trying again.
>> Variable ci has value -2147483648. It should have been within [ 0 .. 1331
>> ]
>>   the position restraint energy is 0 as highlighted. Here's the position
>> restraint file :-
>>  [ position_restraints ]
>> ; atom  type  fx  fy  fz
>> 1 1  1000  1000  5000
>> 5 1  1000  1000  1000
>> 6 1  1000  1000  1000
>> 7 1  1000  1000  1000
>> 8 1  1000  1000  1000
>> 9 1  1000  1000  1000
>>10 1  1000  1000  1000
>> ..
>>
>> whereby the restraint energy is 1000kcal/mol in x, y and z plane. In the
>> log file the position restraint energy is stated as 0.e+00 (as
>> highlighted above).
>> I think that the position restraint is not working fine here. Is there
>> anyways to solve this? did I miss out something here?
>> I would be grateful if anyone can advice me on this.
>>
>>
>>
>> 
>>
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gr

Re: [gmx-users] genbox error at futil.c

[Justin A. Lemkul]

iulek wrote:

Hi!

I am a very beginner, trying to make some dynamics of a protein in a 
water box, after doing some (web) tutorials. I googled first for this 
(possibly simple) error, found one reference, but cannot see it, 
possibly because the gromacs site is under changes.

I ran pdb2gmx and editconf. Then at genbox I get the error:

"
Processing topology

---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330

File input/output error:
RecA_nat_b4em.top
---
"
 


So is the topology in the current working directory?

-Justin



The command line is:
 > genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o 
${MOL}_b4em.gro << eof > genbox.log

eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,

Jorge




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--


Justin A. Lemkul
Ph.D. Candidate
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] Parameters for -Si-Si- chains?

[Semen Esilevsky]

ThanksTsjerk, Google is definitely our best friend :) However, digging for 
parameters and testing the funny mixed force field is not justified in this 
case - the project is small as well as the amount of financing :) So, I whould 
be very grateful if somebody could point me to the ready-to-use -Si-Si- GROMACS 
topologies (if they exists of course).



- Original Message 
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Tuesday, June 23, 2009 11:22:39 AM
Subject: Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:
> Dear All,
> Our colleges asked me to do some rather simple MD of the organic-silicone
> compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
> not so simple because of the force field. Does anybody know about parameters
> for such systems, which are adapted for GROMACS? I've only found -Si-O-
> -parameters in standard ffgmx, which is not what I need. OPLS also has no
> parameters for -Si-Si-Si- chains. Probably somebody know about other force
> fields from which it is possible to transfer missed parameters?
>
> Regards,
> Semen
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] genbox error at futil.c

[iulek]

Hi!

    I am a very beginner, trying to make some dynamics of a protein in
a water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
    I ran pdb2gmx and editconf. Then at genbox I get the error:

"
Processing topology

---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330

File input/output error:
RecA_nat_b4em.top
---
"
    
    The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
    with variable MOL set to RecA_nat 
    The file RecA_nat_b4em.gro is output without problems.
    I am using gromacs 4.0.5 under openSuSE 11.1.
    Thanks,

Jorge



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RE: [gmx-users] pullx.xvg Meaning of output?

[ilona . baldus]

Dear Berk,

Thanks for the quick reply. That leads me to my next questions:
*I used the whole N and C residues for pulling. Is there any way of  
reconstructing the values for the single atoms? Or do you recommend  
only to pull N and C in the first place?
*What does the reference group actually do? Can I simply leave it out?  
Does it influence pulling?  What would be a good reference group? A  
random backbone atom from the middle of the protein?


I'm looking forward to your reply. Thank you very much in advance.

Best wishes, Ilona


Quoting Berk Hess :



Hi,

This is actually not (yet) documented.
0Z is the Z-coordinate of group 0.
1dZ is the the Z-coordinate of group 1 minus the one of group 0.

Berk


Date: Tue, 23 Jun 2009 12:54:37 +0200
From: ilona.bal...@bioquant.uni-heidelberg.de
To: gmx-users@gromacs.org
Subject: [gmx-users] pullx.xvg  Meaning of output?

Hi!

I am trying to understand the output of my pulling simulation:
I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and
-Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.
Since the website is down I cannot check on previous issues, so sorry
for asking the same question again as I already asked last week but
which remained unanswered.

I would appreciate any advice.

Thanks a lot. Ilona
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Ilona Baldus
MPI Stuttgart
INF 276
69120 Heidelberg
Tel.: 06221-5451268
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RE: [gmx-users] pullx.xvg Meaning of output?

[Berk Hess]

Hi,

This is actually not (yet) documented.
0Z is the Z-coordinate of group 0.
1dZ is the the Z-coordinate of group 1 minus the one of group 0.

Berk

> Date: Tue, 23 Jun 2009 12:54:37 +0200
> From: ilona.bal...@bioquant.uni-heidelberg.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pullx.xvg  Meaning of output?
> 
> Hi!
> 
> I am trying to understand the output of my pulling simulation:
> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and  
> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.  
> Since the website is down I cannot check on previous issues, so sorry  
> for asking the same question again as I already asked last week but  
> which remained unanswered.
> 
> I would appreciate any advice.
> 
> Thanks a lot. Ilona
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Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Justin A. Lemkul]

Bing Bing wrote:
Hi! I'm a postgraduate student from Malaysia and currently facing energy 
minimization problem for my membrane system.
I'm trying to perform energy minimization for an empty POPC membrane 
with position restraint on the lipid. Minimization stop due to inf Fmax. 
And I noticed that in the log file as below:-
 
 
Initiating Steepest Descents

Max number of connections per atom is 25
Total number of connections is 84976
Max number of graph edges per atom is 4
Total number of graph edges is 22896
Going to use C-settle (2460 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=  100
Grid: 11 x 11 x 11 cells
   Step   Time Lambda
  00.00.0
   Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  Improper Dih.
1.64082e+051.71875e+044.06560e+036.45104e+038.36392e+03
  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.
   2.12067e-314   2.12067e-314   -1.58963e+04   -1.05392e+05   -1.15292e+05
 Position Rest.  Potential Pressure (bar)
0.0e+00   -3.64297e+04nan



From the looks of some of these energies (i.e., LJ-14, Coulomb-14), it looks 
like something is severely wrong with your starting structure, and applying 
position restraints probably isn't helping.


Try the minimization without restraints and see if it works.

Also, have you set the appropriate "define" line in the .mdp file, corresponding 
to what is prescribed in the .top?


-Justin


---
Program mdrun_d, VERSION 4.0.5
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ]
 
 
the position restraint energy is 0 as highlighted. Here's the position 
restraint file :-
 
[ position_restraints ]

; atom  type  fx  fy  fz
 1 1  1000  1000  5000
 5 1  1000  1000  1000
 6 1  1000  1000  1000
 7 1  1000  1000  1000
 8 1  1000  1000  1000
 9 1  1000  1000  1000
10 1  1000  1000  1000
..

whereby the restraint energy is 1000kcal/mol in x, y and z plane. In the 
log file the position restraint energy is stated as 0.e+00 (as 
highlighted above).
I think that the position restraint is not working fine here. Is there 
anyways to solve this? did I miss out something here?

I would be grateful if anyone can advice me on this.
 
 
 

 





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--


Justin A. Lemkul
Ph.D. Candidate
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] simulation of protein in presence of ATP

[Justin A. Lemkul]

nikhil damle wrote:
Thanks a lot for kind help. I reached till grompp before minimizing 
energy of the system where I received an error msg as "Invalid order for 
directive defaults: filename; line x" !!! what is 
the meaning of this error ? Is it something to do with path variable 
problem or writing things in improper order ?




Probably, if you've processed your protein with pdb2gmx as well as the ATP 
molecule, you have two .top files, each of which contains an #include statement 
for your force field, so you're duplicating these entries.


Without any information about the contents of your .top(s) or how you've 
actually built things, this is just a guess.


See here:

http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

-Justin


Nikhil


*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Tuesday, 23 June, 2009 12:35:12 PM
*Subject:* Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
 > Hi,
 >  We can use max 4 coloumns for naming atoms. But .rtp file has 5 
coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now 
the error is "atom N not found in residue 1ATP while combining tdb and rtp"


pdb2gmx tries to cap termini of peptides automatically, but this isn't a 
peptide. So look at pdb2gmx -h and choose the option that will allow you 
to interactively choose that no terminal capping needs to take place.


Mark

 > 
 > *From:* Mark Abraham >
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
 > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
 >
 > nikhil damle wrote:
 >  > Hi,
 >  >
 >  >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb 
to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" 
I converted HETATM tag to ATOM tag. Still same error msg. Please find 
ATP.pdb file attached herewith.

 >
 > You've broken the PDB format, which encodes the information in 
fixed-column style. See 
http://www.wwpdb.org/documentation/format32/v3.2.html

 >
 > Mark
 > ___
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[gmx-users] pullx.xvg Meaning of output?

[ilona . baldus]

Hi!

I am trying to understand the output of my pulling simulation:
I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and  
-Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.  
Since the website is down I cannot check on previous issues, so sorry  
for asking the same question again as I already asked last week but  
which remained unanswered.


I would appreciate any advice.

Thanks a lot. Ilona
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[gmx-users] Re: How to freeze the atoms?

[Vitaly V. Chaban]

>
> Dear all
>    I attach 8 carbonyl groups onto a
> carbon nanotube (CNT). Each carbonyl group is considered as a residue named
> "Car" and each carbon atom in the CNT is considered as a residue named
> "Gr1". In the mdp file, the freezegrps are Gr1 and Car, and the freezedim
> are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in the
> carbonyl groups are fixed in three dimensions and they can not move in any
> direction. However, when I made the energy minimization, the coordinates of
> C and O in carbonyl groups changed.
>   How can I really fix the atoms? Look forward
> for your suggestions!
>

All the atoms which relate to your frozen groups should be non-movable
during MD.

>the coordinates of C and O in carbonyl groups changed.

Only ones of CHO changed? And the CNT itself is nonmovable? Check your
groups please.


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
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Re: [gmx-users] simulation of protein in presence of ATP

[nikhil damle]

Thanks a lot for kind help. I reached till grompp before minimizing energy of 
the system where I received an error msg as "Invalid order for directive 
defaults: filename; line x" !!! what is the meaning of this 
error ? Is it something to do with path variable problem or writing things in 
improper order ?

Nikhil





From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Tuesday, 23 June, 2009 12:35:12 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> Hi,
>  We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn 
> atom names (AO1PG etc) That i modified to 4 letter name. But now the error is 
> "atom N not found in residue 1ATP while combining tdb and rtp"

pdb2gmx tries to cap termini of peptides automatically, but this isn't a 
peptide. So look at pdb2gmx -h and choose the option that will allow you to 
interactively choose that no terminal capping needs to take place.

Mark

> 
> *From:* Mark Abraham 
> *To:* Discussion list for GROMACS users 
> *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
> 
> nikhil damle wrote:
>  > Hi,
>  >
>  >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to 
> pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I 
> converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb 
> file attached herewith.
> 
> You've broken the PDB format, which encodes the information in fixed-column 
> style. See http://www.wwpdb.org/documentation/format32/v3.2.html
> 
> Mark
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[gmx-users] Problem in energy minimization for a empty membrane system

[Bing Bing]

Hi! I'm a postgraduate student from Malaysia and currently facing energy
minimization problem for my membrane system.
I'm trying to perform energy minimization for an empty POPC membrane with
position restraint on the lipid. Minimization stop due to inf Fmax. And I
noticed that in the log file as below:-


Initiating Steepest Descents
Max number of connections per atom is 25
Total number of connections is 84976
Max number of graph edges per atom is 4
Total number of graph edges is 22896
Going to use C-settle (2460 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=  100
Grid: 11 x 11 x 11 cells
   Step   Time Lambda
  00.00.0
   Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  Improper Dih.
1.64082e+051.71875e+044.06560e+036.45104e+038.36392e+03
  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.
   2.12067e-314   2.12067e-314   -1.58963e+04   -1.05392e+05   -1.15292e+05
 Position Rest.  Potential Pressure (bar)
0.0e+00   -3.64297e+04nan

---
Program mdrun_d, VERSION 4.0.5
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ]


the position restraint energy is 0 as highlighted. Here's the position
restraint file :-

[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  1000  1000  5000
 5 1  1000  1000  1000
 6 1  1000  1000  1000
 7 1  1000  1000  1000
 8 1  1000  1000  1000
 9 1  1000  1000  1000
10 1  1000  1000  1000
..

whereby the restraint energy is 1000kcal/mol in x, y and z plane. In the log
file the position restraint energy is stated as 0.e+00 (as highlighted
above).
I think that the position restraint is not working fine here. Is there
anyways to solve this? did I miss out something here?
I would be grateful if anyone can advice me on this.
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Re: [gmx-users] How to freeze the atoms?

[Mark Abraham]

toby10222...@sina.com wrote:

 Dear all

   I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each 
carbonyl group is considered as a residue named "Car" and each carbon 
atom in the CNT is considered as a residue named "Gr1". In the mdp file, 
the freezegrps are Gr1 and Car, and the freezedim are Y Y Y Y Y Y. Does 
it mean that all the C in the CNT and C and O in the carbonyl groups are 
fixed in three dimensions and they can not move in any direction. 
However, when I made the energy minimization, the coordinates of C and O 
in carbonyl groups changed.


  How can I really fix the atoms? Look forward for your suggestions!


group names and residue names only mean the same thing if you've 
constructed your groups accordingly.


Mark
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[gmx-users] How to freeze the atoms?

[toby10222224]

 Dear all
   I attach 8 carbonyl groups onto a carbon 
nanotube (CNT). Each carbonyl group is considered as a residue named "Car" and 
each carbon atom in the CNT is considered as a residue named "Gr1". In the 
mdp file, the freezegrps are Gr1 and Car, and the freezedim are Y Y Y Y Y Y. 
Does it mean that all the C in the CNT and C and O in the carbonyl groups are 
fixed in three dimensions and they can not move in any direction. However, when 
I made the energy minimization, the coordinates of C and O in carbonyl groups 
changed.
  How can I really fix the atoms? Look forward for 
your suggestions!
Yours Sincerely
Toby___
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RE: [gmx-users] How to increase the number of parameters in dihedral angle potentials?

[Berk Hess]

Hi,

I already answered this mail, but somehow for a small fraction of
the mails I reply to hotmail replies to the user, not to the list.
Here is my answer:

You can't do this easily.
The current maximum for the number of parameters per interaction is 6.
If you really want to, you could increase this, as well as NR_RBDIHS
in include/types/idef.h. This would make your tpr files incompatible
with the standard release binaries.

Another option would be to use tabulated dihedral functions,
then you can do anything you want (see the manual).

Berk


> Date: Tue, 23 Jun 2009 10:16:45 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to increase the number of parameters in dihedral 
> angle potentials?
> 
> bh...@princeton.edu wrote:
> > Dear all,
> > 
> > This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans 
> > function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a 
> > function of summation over 8 terms, that is, 8 parameters from C0 to C7. I 
> > tried to add the values of  the two additional pamameters at the end of 
> > each lines in the section of dihedral angles in the 'molecule.itp' file. 
> > The 'grompp' command then gave an error information, saying there could 
> > only be either 6 or 12 parameters for Ryckaert-Bellemans potentials. 
> 
> If you read the description of R-B in the manual, it only allows for 
> 6-parameter R-B. It's not obvious (see footnote to table 5.4, at least), 
> but the other are for free energy calculations that might be varying 
> these parameters.
> 
> >So I added 4 zeros for the rest 4 parameters in 'molecule.itp'. Now, the 
> >'grompp' command did not gave error information any more and I run the 
> >simulation with a 12-parameter Ryckaert-Bellemans potential. The problem is 
> >that the trajectory obtained from 12-parameter RB potential is exactly the 
> >same as the trajectory having generated by 6-parameter RB potential. That 
> >means the newly added 6 parameter values can not be recognized by GROMACS. 
> >Has anyone met with such kind of problems? 
> 
> Hence, your observations. Since you're not running FE, the 7th and 8th 
> are never being used for anything.
> 
> >What did you do to make GROMACS recognize 6 more parameters in RB 
> >potentials? 
> 
> You can't. You would have to either implement your own bonded function, 
> or use a table lookup for this bonded interaction. See manual section 4.2.13
> 
> Mark
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Re: [gmx-users] Parameters for -Si-Si- chains?

[Tsjerk Wassenaar]

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:
> Dear All,
> Our colleges asked me to do some rather simple MD of the organic-silicone
> compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
> not so simple because of the force field. Does anybody know about parameters
> for such systems, which are adapted for GROMACS? I've only found -Si-O-
> -parameters in standard ffgmx, which is not what I need. OPLS also has no
> parameters for -Si-Si-Si- chains. Probably somebody know about other force
> fields from which it is possible to transfer missed parameters?
>
> Regards,
> Semen
>
>
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Parameters for -Si-Si- chains?

[Semen Esilevsky]

Dear All,
Our colleges asked me to do some rather simple MD of the organic-silicone 
compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be 
not so simple because of the force field. Does anybody know about parameters 
for such systems, which are adapted for GROMACS? I've only found -Si-O- 
-parameters in standard ffgmx, which is not what I need. OPLS also has no 
parameters for -Si-Si-Si- chains. Probably somebody know about other force 
fields from which it is possible to transfer missed parameters?

Regards,
Semen



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Re: [gmx-users] simulation of protein in presence of ATP

[Mark Abraham]

nikhil damle wrote:

Hi,
 
We can use max 4 coloumns for naming atoms. But .rtp file has 5 
coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now 
the error is "atom N not found in residue 1ATP while combining tdb and rtp"


pdb2gmx tries to cap termini of peptides automatically, but this isn't a 
peptide. So look at pdb2gmx -h and choose the option that will allow you 
to interactively choose that no terminal capping needs to take place.


Mark



*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Tuesday, 23 June, 2009 11:16:26 AM
*Subject:* Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
 > Hi,
 >
 >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to 
pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I 
converted HETATM tag to ATOM tag. Still same error msg. Please find 
ATP.pdb file attached herewith.


You've broken the PDB format, which encodes the information in 
fixed-column style. See 
http://www.wwpdb.org/documentation/format32/v3.2.html


Mark
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