[gmx-users] Switch - Shift function electrostatics

[Emanuel Peter]

Dear Gromacs-users,

At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.

I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.

It is clear to me what Shift and PME means principally, but I ask myself
 which electrostatic algorithm is used by Cut-off.
I know that Cut-off means a twin-range-electrostatics calculation with
rlist as the first range and r_coulomb as the second range. Both are
calculated within different frequencies. Is that true ?

In my .log file it is mentioned that when using Cut-off a default value
r_coulombswitch equal to 0 is set. It is the same in the case of
r_vdwswitch.

Does that mean that I use in this special case a switch function which
switches at 0 nm which represents in this case a shift-function that
shifts my electrostatic potential in such a way, that it decays to zero
at r_coulomb?
I think this means that I used a shift-function which is calculated
within the twin-range-electrostatics scheme.
Is this true?

What disadvantages does the twin-range-electrostatics calculation
have in comparison to PME?
Is it true that PME could stabilize my system artificially?

Now another question:

Some people who perform molecular-dynamics calculations are stabilizing
the dihedral angles in the forcefield to avoid 'unrealistical'
fluctuations of their protein. Is this a reasonable way to simulate a
protein?
Is it also reasonable to heat up a crystal -.pdb structure, determined
by x-ray, slowly from 50 K up to 300 K in a couple of steps?
Does this have any purpose or is this just a non proven setup of my
structure?

Thanks for your good advice in advance!

Best regards,

Emanuel Peter

Institute of Phys. and Theor. Chemistry
93053 Regensburg
Germany











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Re: [gmx-users] Switch - Shift function electrostatics

[David van der Spoel]

Emanuel Peter wrote:

Dear Gromacs-users,

At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.

I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.

It is clear to me what Shift and PME means principally, but I ask myself
 which electrostatic algorithm is used by Cut-off.
I know that Cut-off means a twin-range-electrostatics calculation with
rlist as the first range and r_coulomb as the second range. Both are
calculated within different frequencies. Is that true ?

In my .log file it is mentioned that when using Cut-off a default value
r_coulombswitch equal to 0 is set. It is the same in the case of
r_vdwswitch.

Does that mean that I use in this special case a switch function which
switches at 0 nm which represents in this case a shift-function that
shifts my electrostatic potential in such a way, that it decays to zero
at r_coulomb?
I think this means that I used a shift-function which is calculated
within the twin-range-electrostatics scheme.
Is this true?

What disadvantages does the twin-range-electrostatics calculation
have in comparison to PME?
Is it true that PME could stabilize my system artificially?


No, it is the other way around. Cut-offs are bad.
Check:
J. Chem. Theor. Comp. 2 pp. 1-11 (2006)



Now another question:

Some people who perform molecular-dynamics calculations are stabilizing
the dihedral angles in the forcefield to avoid 'unrealistical'
fluctuations of their protein. Is this a reasonable way to simulate a
protein?
No, you are changing the force field in that way. I haven't heard of 
this previously.




Is it also reasonable to heat up a crystal -.pdb structure, determined
by x-ray, slowly from 50 K up to 300 K in a couple of steps?
Does this have any purpose or is this just a non proven setup of my
structure?

Thanks for your good advice in advance!

Best regards,

Emanuel Peter

Institute of Phys. and Theor. Chemistry
93053 Regensburg
Germany











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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] Fes cluster

[subarna thakur]

Hello 
The protein I am considering is a homodimer with two chains with a Fe4S4 
cluster situated at the interface of two chains with connections with both the 
chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster 
and .top of the protein with pdb2gmx command.The .top file is like this-
-;
; File '1braf.top' was generated
; By user: root (0)
; On host: localhost.localdomain
; At date: Mon Jul 27 13:12:40 2009
;
; This is your topology file
; "I Have a Bad Case Of Purple Diarrhea" (Urban Dance Squad)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include chain topologies
#include "1braf_A.itp"
#include "1braf_B.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
-
I want to know how do I include the Fe4S4 .itp file in the topology file of the 
protein and How do I include the connect information of the protein and FES 
cluster.
Regards
Subarna


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[gmx-users] diffusion, g_msd and trestart

[Enemark Soeren]

Dear all,

I am trying to calculate diffusion coefficients for a system of (30)
glycine molecules in a box with (1000) water.

 

After running:

g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx

 

I get a list of diffusion coefficients - one for each glycine molecule.
I then calculate the average and the stdev:

 

Average=1.004

Stdev=0.7661

 

My problem is that the stdev is very great! More than +/- 75% of the
average value.

Why is that?

 

Also, what is the reason for the trestart=10 default value? Shouldn't it
be better to have trestart=1, if my xtc file is saved every 1 ps?

 

Thanks,

Soren Enemark

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Re: [gmx-users] diffusion, g_msd and trestart

[David van der Spoel]

Enemark Soeren wrote:

Dear all,

I am trying to calculate diffusion coefficients for a system of (30) 
glycine molecules in a box with (1000) water.


 


After running:

g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx

 

I get a list of diffusion coefficients – one for each glycine molecule. 
I then calculate the average and the stdev:


 


Average=1.004

Stdev=0.7661

 

My problem is that the stdev is very great! More than +/- 75% of the 
average value.


Why is that?


Short simulation most likely. Since these things are big it takes a long 
time to equilibrate.




 

Also, what is the reason for the trestart=10 default value? Shouldn’t it 
be better to have trestart=1, if my xtc file is saved every 1 ps?


No, because there is correlation in the system. Ideally you would take 
this time to be longer than the correlation time. You could try to find 
an estimate of that from the velocity autocorrelation.





 


Thanks,

Soren Enemark




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] Switch - Shift function electrostatics

[Ran Friedman]

David van der Spoel wrote:
> Emanuel Peter wrote:
>> Dear Gromacs-users,
>>
>> At the moment I have a question which regards the different
>> electrostatic algorithms mentioned in the Gromacs-manual.
>>
>> I did some simulations and I tried three different electrostatic
>> algorithms: Cut-off, Shift and PME.
>>
>> It is clear to me what Shift and PME means principally, but I ask myself
>>  which electrostatic algorithm is used by Cut-off.
>> I know that Cut-off means a twin-range-electrostatics calculation with
>> rlist as the first range and r_coulomb as the second range. Both are
>> calculated within different frequencies. Is that true ?
>>
>> In my .log file it is mentioned that when using Cut-off a default value
>> r_coulombswitch equal to 0 is set. It is the same in the case of
>> r_vdwswitch.
>>
>> Does that mean that I use in this special case a switch function which
>> switches at 0 nm which represents in this case a shift-function that
>> shifts my electrostatic potential in such a way, that it decays to zero
>> at r_coulomb?
>> I think this means that I used a shift-function which is calculated
>> within the twin-range-electrostatics scheme.
>> Is this true?
>>
>> What disadvantages does the twin-range-electrostatics calculation
>> have in comparison to PME?
>> Is it true that PME could stabilize my system artificially?
>>
> No, it is the other way around. Cut-offs are bad.
> Check:
> J. Chem. Theor. Comp. 2 pp. 1-11 (2006)
>
>
>> Now another question:
>>
>> Some people who perform molecular-dynamics calculations are stabilizing
>> the dihedral angles in the forcefield to avoid 'unrealistical'
>> fluctuations of their protein. Is this a reasonable way to simulate a
>> protein?
> No, you are changing the force field in that way. I haven't heard of
> this previously.
I guess you mean CMAP in CHARMM.
You can check out the relevant paper, which also includes details about
some other force fields.

Ran.
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RE: [gmx-users] diffusion, g_msd and trestart

[Berk Hess]

> Date: Mon, 27 Jul 2009 11:12:16 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] diffusion, g_msd and trestart
> 
> Enemark Soeren wrote:
> > Dear all,
> > 
> > I am trying to calculate diffusion coefficients for a system of (30) 
> > glycine molecules in a box with (1000) water.
> > 
> >  
> > 
> > After running:
> > 
> > g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx
> > 
> >  
> > 
> > I get a list of diffusion coefficients – one for each glycine molecule. 
> > I then calculate the average and the stdev:
> > 
> >  
> > 
> > Average=1.004
> > 
> > Stdev=0.7661
> > 
> >  
> > 
> > My problem is that the stdev is very great! More than +/- 75% of the 
> > average value.
> > 
> > Why is that?
> 
> Short simulation most likely. Since these things are big it takes a long 
> time to equilibrate.
> 

Also it depends on what you expect.
stdev is not a standard error estimate of the average.
It is the spread around the average for all molecules.
If all the msd values of the molecules are uncorrelated,
which they might or might not be, the error estimate would be stdev/sqrt(30).

Berk

> > 
> >  
> > 
> > Also, what is the reason for the trestart=10 default value? Shouldn’t it 
> > be better to have trestart=1, if my xtc file is saved every 1 ps?
> 
> No, because there is correlation in the system. Ideally you would take 
> this time to be longer than the correlation time. You could try to find 
> an estimate of that from the velocity autocorrelation.
> 
> 
> > 
> >  
> > 
> > Thanks,
> > 
> > Soren Enemark
> > 
> > 
> > 
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
> ___
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RE: [gmx-users] diffusion, g_msd and trestart

[Enemark Soeren]

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart

Enemark Soeren wrote:
> Dear all,
> 
> I am trying to calculate diffusion coefficients for a system of (30) 
> glycine molecules in a box with (1000) water.
> 
>  
> 
> After running:
> 
> g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx
> 
>  
> 
> I get a list of diffusion coefficients - one for each glycine
molecule. 
> I then calculate the average and the stdev:
> 
>  
> 
> Average=1.004
> 
> Stdev=0.7661
> 
>  
> 
> My problem is that the stdev is very great! More than +/- 75% of the 
> average value.
> 
> Why is that?

Short simulation most likely. Since these things are big it takes a long

time to equilibrate.

> 
>  
> 
> Also, what is the reason for the trestart=10 default value? Shouldn't
it 
> be better to have trestart=1, if my xtc file is saved every 1 ps?

No, because there is correlation in the system. Ideally you would take 
this time to be longer than the correlation time. You could try to find 
an estimate of that from the velocity autocorrelation.


> 
>  
> 
> Thanks,
> 
> Soren Enemark
> 
> 
>

> 
> ___
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] Fes cluster

[Mark Abraham]

subarna thakur wrote:
Hello 
The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this-

-;
; File '1braf.top' was generated
; By user: root (0)
; On host: localhost.localdomain
; At date: Mon Jul 27 13:12:40 2009
;
; This is your topology file
; "I Have a Bad Case Of Purple Diarrhea" (Urban Dance Squad)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include chain topologies
#include "1braf_A.itp"
#include "1braf_B.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
-
I want to know how do I include the Fe4S4 .itp file in the topology file of the protein 


Do you have one? Does your force field have suitable parameters for this 
moiety?



and How do I include the connect information of the protein and FES cluster.


You will need to understand parts of chapter 5 of the manual thoroughly. 
Work on understanding a simple diglycine .top file first.


Mark
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RE: [gmx-users] diffusion, g_msd and trestart

[Enemark Soeren]

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart

Enemark Soeren wrote:
> Dear all,
> 
> I am trying to calculate diffusion coefficients for a system of (30) 
> glycine molecules in a box with (1000) water.
> 
>  
> 
> After running:
> 
> g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx
> 
>  
> 
> I get a list of diffusion coefficients - one for each glycine
molecule. 
> I then calculate the average and the stdev:
> 
>  
> 
> Average=1.004
> 
> Stdev=0.7661
> 
>  
> 
> My problem is that the stdev is very great! More than +/- 75% of the 
> average value.
> 
> Why is that?

Short simulation most likely. Since these things are big it takes a long

time to equilibrate.

My simulation is 10ns long with xtc saved every 1 ps. I thought I had
enough data!?
How long is "long time"?

> 
>  
> 
> Also, what is the reason for the trestart=10 default value? Shouldn't
it 
> be better to have trestart=1, if my xtc file is saved every 1 ps?

No, because there is correlation in the system. Ideally you would take 
this time to be longer than the correlation time. You could try to find 
an estimate of that from the velocity autocorrelation.

So, I must run velocity autocorrelation to find out when the velocities
become uncorrelated, and then use this time as my trestart?

Thanks,
Soren

> 
>  
> 
> Thanks,
> 
> Soren Enemark
> 
> 
>

> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] diffusion, g_msd and trestart

[David van der Spoel]

Enemark Soeren wrote:


-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart

Enemark Soeren wrote:

Dear all,

I am trying to calculate diffusion coefficients for a system of (30) 
glycine molecules in a box with (1000) water.


 


After running:

g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx

 


I get a list of diffusion coefficients - one for each glycine
molecule. 

I then calculate the average and the stdev:

 


Average=1.004

Stdev=0.7661

 

My problem is that the stdev is very great! More than +/- 75% of the 
average value.


Why is that?


Short simulation most likely. Since these things are big it takes a long

time to equilibrate.

My simulation is 10ns long with xtc saved every 1 ps. I thought I had
enough data!?
How long is "long time"?

 


Also, what is the reason for the trestart=10 default value? Shouldn't
it 

be better to have trestart=1, if my xtc file is saved every 1 ps?


No, because there is correlation in the system. Ideally you would take 
this time to be longer than the correlation time. You could try to find 
an estimate of that from the velocity autocorrelation.


So, I must run velocity autocorrelation to find out when the velocities
become uncorrelated, and then use this time as my trestart?
.


That would be a way (and the VACF also gives you a diffusion constant), 
you can also check the histogram visually for different run times. It 
seems that your solution does have a lot of amino acids, which probably 
means high viscosity and slow diffusion, and hence long time to 
equilibrate. Looking at the system MSD for all the Gly may also show you 
when the MSD curve becomes linear, you can use this as well as an 
estimate for the trestart.




Thanks,
Soren

 


Thanks,

Soren Enemark






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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] GHrace install

[Samik Bhattacharya]

hi alli'm facing  alot of trouble in installing grace in my redhat machine. its 
always complaining about Motiff API. ive installed Lesstiff but even afetr that 
grace is not getting installed...i can't make out how to install it? is there 
any problem in the path? should i've to set path before grace install. i've 
gone through several pages about grace installation but with no effect.ac 
anyone pls tell me how to install Grace in Fedora of Redhat?
thanking you all
Shamik



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Re: [gmx-users] GHrace install

[Jussi Lehtola]

On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote:
> hi alli'm facing  alot of trouble in installing grace in my redhat
> machine. its always complaining about Motiff API.. ive installed
> Lesstiff but even afetr that grace is not getting installedi can't
> make out how to install it? is there any problem in the path? should
> i've to set path before grace install. i've gone through several pages
> about grace installation but with no effect.ac anyone pls tell me how
> to install Grace in Fedora of Redhat?

You should avoid compiling software yourself, because that beats the
whole idea of having a) a distribution that has ready-to-use software
and b) a package management system that makes upgrades possible.

In Fedora
# yum -y install grace

In RHEL, first enable the Fedora EPEL repository with
# rpm -Uvh \
http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm
and then install grace with
# yum -y install grace

Then you can run grace with $ xmgrace
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--

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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Lee Soin]

I see in the .top file generated by pdb2gmx:
[ pairs ]
;  aiaj functc0c1c2c3

The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand for
respectively? Thanks!


2009/7/27 Mark Abraham 

> Lee Soin wrote:
>
>> My problem is actually as follows:
>>
>
> Please describe in as full detail as reasonable the first time :-)
>
>  I have three groups of atoms: A, B and C. Now I want to keep full
>> interaction between A-B and A-C, but only retain the repulsive part of VDW
>> interaction between B-C. I'm using the OPLS force field. It seems to me
>> that
>> the parameters for OPLS in the .itp files are specified for each atom, so
>> is
>> there any way to treat the interaction pairwise?
>>
>
> Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That
> will be tedious if there are many such atoms. Read parts of chapter 5.
>
> Probably, no force field was parameterized to reproduce whatever it is
> you're trying to observe.
>
>
> Mark
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-- 
SUN Li
Department of Physics
Nanjing University, China
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RE: [gmx-users] GHrace install

[jimkress_58]

If you are using a vanilla RedHat system, the yum method will work.
However, if you are using a prepackaged clustering environment (like ROCKS)
you may break it.

All you nee to know to install grace is the location of the headers and
libraries for Lesstiff.  You then supply them to grace as a part of the
./configure command and things should go smoothly.

It's unfortunate the person who wrote and maintains grace is unwilling to
provide this information to the people that want to use grace.  However, you
can't stop people from being jerks.  That's why I'd prefer gromacs use a
different plotting package like gnuplot.

Jim

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Samik Bhattacharya
Sent: Monday, July 27, 2009 7:19 AM
To: Gromacs
Subject: [gmx-users] GHrace install

hi alli'm facing  alot of trouble in installing grace in my redhat machine.
its always complaining about Motiff API.. ive installed Lesstiff but even
afetr that grace is not getting installedi can't make out how to install
it? is there any problem in the path? should i've to set path before grace
install. i've gone through several pages about grace installation but with
no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat?
thanking you all
Shamik




Looking for local information? Find it on Yahoo! Local
 

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[gmx-users] POSITION-RESTRAIN

[Morteza Khabiri]

Dear gmxusers.

I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
 Atom index (53) in position_restraints out of bounds (1-52)
I found the similar error in the mailing list and they suggested probably
the place of restraint itp file which was included in  topology file is
wrong.  However, I tried several positions for restraint itp but I think
it is not the
solution. Do you have any other suggestion about this problem??

Thanks



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Re: [gmx-users] POSITION-RESTRAIN

[Mark Abraham]

Morteza Khabiri wrote:

Dear gmxusers.

I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
 Atom index (53) in position_restraints out of bounds (1-52)
I found the similar error in the mailing list and they suggested probably
the place of restraint itp file which was included in  topology file is
wrong.  However, I tried several positions for restraint itp but I think
it is not the
solution. Do you have any other suggestion about this problem??


You're using a [ position_restraints ] directive that requires at least 
53 atoms in a position where only 52 are defined. There are various 
explanations, including #including in the wrong place, or #including a 
wrong file. Look carefully at a correct example.


Mark
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Re: [gmx-users] GHrace install

[Mark Abraham]

jimkress_58 wrote:

If you are using a vanilla RedHat system, the yum method will work.
However, if you are using a prepackaged clustering environment (like ROCKS)
you may break it.

All you nee to know to install grace is the location of the headers and
libraries for Lesstiff.  You then supply them to grace as a part of the
./configure command and things should go smoothly.

It's unfortunate the person who wrote and maintains grace is unwilling to
provide this information to the people that want to use grace.  However, you
can't stop people from being jerks.  That's why I'd prefer gromacs use a
different plotting package like gnuplot.


Agreed, although it is straightforward to use gnuplot anyway. See 
http://oldwiki.gromacs.org/index.php/Graphing_Data


Mark
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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Mark Abraham]

Lee Soin wrote:

I see in the .top file generated by pdb2gmx:
[ pairs ]
;  aiaj functc0c1c2c3

The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand for
respectively? Thanks!


No, they're two pairs of VDW parameters, one pair each for two possible 
states for a free-energy calculation. The tables in chapter 5 imply 
this, but it is not at all obvious to a newcomer.



Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That
will be tedious if there are many such atoms. Read parts of chapter 5.


You should still do this.

Mark
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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Lee Soin]

So there is no place to specify electrostatic interactions for pair
interactions?



2009/7/27 Mark Abraham 

> Lee Soin wrote:
>
>> I see in the .top file generated by pdb2gmx:
>> [ pairs ]
>> ;  aiaj functc0c1c2c3
>>
>> The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3.
>> Do
>> c2 and c3 parametrize electrostatic interactions? And what do they stand
>> for
>> respectively? Thanks!
>>
>
> No, they're two pairs of VDW parameters, one pair each for two possible
> states for a free-energy calculation. The tables in chapter 5 imply this,
> but it is not at all obvious to a newcomer.
>
>  Yes, use [ pairs ] directives to overrride the atomtype-based lookup.
>>> That
>>> will be tedious if there are many such atoms. Read parts of chapter 5.
>>>
>>
> You should still do this.
>
>
> Mark
> ___
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-- 
SUN Li
Department of Physics
Nanjing University, China
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[gmx-users] doubt - how to fix all atoms ?

[Luis Paulo]

Please

 I need  to fix all atoms of a proetin and I need to calculte the initital
enregy without to exceute septs of dynsmics.
How can i do this ?

Thanks
best regrads
luis Scott

2009/7/27 

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>
>
> Today's Topics:
>
>   1. GHrace install (Samik Bhattacharya)
>   2. Re: GHrace install (Jussi Lehtola)
>   3. Re: About exclusion of non-bonded interaction for pairs   of
>  energy groups (Lee Soin)
>   4. RE: GHrace install (jimkress_58)
>   5. POSITION-RESTRAIN (Morteza Khabiri)
>   6. Re: POSITION-RESTRAIN (Mark Abraham)
>   7. Re: GHrace install (Mark Abraham)
>   8. Re: About exclusion of non-bonded interaction for pairs   of
>  energy groups (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Mon, 27 Jul 2009 16:48:57 +0530 (IST)
> From: Samik Bhattacharya 
> Subject: [gmx-users] GHrace install
> To: Gromacs 
> Message-ID: <224940.85000...@web95411.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hi alli'm facing  alot of trouble in installing grace in my redhat machine.
> its always complaining about Motiff API. ive installed Lesstiff but even
> afetr that grace is not getting installed...i can't make out how to install
> it? is there any problem in the path? should i've to set path before grace
> install. i've gone through several pages about grace installation but with
> no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat?
> thanking you all
> Shamik
>
>
>
>  See the Web's breaking stories, chosen by people like you. Check
> out Yahoo! Buzz. http://in.buzz.yahoo.com/
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a13124cb/attachment-0001.html
>
> --
>
> Message: 2
> Date: Mon, 27 Jul 2009 14:28:31 +0300
> From: Jussi Lehtola 
> Subject: Re: [gmx-users] GHrace install
> To: Discussion list for GROMACS users 
> Message-ID: <1248694111.5152.2.ca...@hawking.theorphys.helsinki.fi>
> Content-Type: text/plain
>
> On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote:
> > hi alli'm facing  alot of trouble in installing grace in my redhat
> > machine. its always complaining about Motiff API.. ive installed
> > Lesstiff but even afetr that grace is not getting installedi can't
> > make out how to install it? is there any problem in the path? should
> > i've to set path before grace install. i've gone through several pages
> > about grace installation but with no effect.ac anyone pls tell me how
> > to install Grace in Fedora of Redhat?
>
> You should avoid compiling software yourself, because that beats the
> whole idea of having a) a distribution that has ready-to-use software
> and b) a package management system that makes upgrades possible.
>
> In Fedora
> # yum -y install grace
>
> In RHEL, first enable the Fedora EPEL repository with
> # rpm -Uvh \
>
> http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm
> and then install grace with
> # yum -y install grace
>
> Then you can run grace with $ xmgrace
> --
> --
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.leht...@helsinki.fi, p. 191 50632
> --
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.leht...@helsinki.fi
> --
>
>
>
> --
>
> Message: 3
> Date: Mon, 27 Jul 2009 21:56:08 +0800
> From: Lee Soin 
> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for
>pairs   of energy groups
> To: Discussion list for GROMACS users 
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I see in the .top file generated by pdb2gmx:
> [ pairs ]
> ;  aiaj functc0c1 

[gmx-users] Huge acceleration needed to reproduce results!

[Jennifer Williams]

Hello users,

I am trying to reproduce a calculation that I carried out in DL_POLY.  
It is to calculate the transport diffusion coefficient for CH4 in a  
frozen mesoporous silica.


In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per  
mole per angstrom). This equates to 10 dl_poly internal units which I  
add in this way at each timestep;


Fsum = Fsum + Fex

In Gromacs, I want to apply the same force as I used in DL_POLY so I  
calculated the required acceleration using F=ma. Where I took the mass  
to be the mass of one molecule of methane (16 a.m.u).


The final value for acceleration that I came up with (which  
corresponds to a force of 0.1kj mol-1 A-1 on each molecule) was 0.0625  
nm ps-2.


The first hiccup was when I used this value, the MSD was negative  
(though linear in the negative region of the graph). I assumed that  
this had something to do with the orientation of the unit cell and  
tried applying 0.0   0.0  -0.0625. The plot then looked much better.


The problem is when I calculate the Mean displacement of the CH4  
molecules. (I do this using a slightly altered version of the g_msd  
code). The Mean displacement  from gromacs is very different to that  
which I calculate using DL_POLY,


Gromacs gives 95.0, dl_poly 21347.0.

The MSD however (where I don?t add an acceleration are similar) so the  
problem lies with the force I am adding.


To test that it wasn?t some bug in my code to calculate the Mean  
displacement, I also looked at how the acceleration/force altered the  
MSD in DL_POLY and gromacs.


In DL_POLY, adding an external force of 0.1kj mol-1 A-1 would change  
the MSD of methane by 3 orders of magnitude compared to a run with no  
force added.


My equivalent acceleration of -0.0625 in gromacs, in comparison,  
barely changes the MSD from that of a run with no acceleration added.  
In fact it takes an acceleration of -200 in the z direction to cause  
such a difference in the Ds coefficients between runs with and without  
acceleration.


Does anyone have any idea what is going on here? An acceleration of  
200 ps nm-2 surely is not reasonable is it?. It seems very large  
compared to the example in the manual of 0.1. This would then imply  
that my back of the envelope calculation for relating force and  
acceleration is wrong. Am I missing something? I?m quite sure that the  
force I am adding in DL_POLY is equivalent to 0.1 kJ mol-1 A-1 so why  
are my methane molecules moving so much less in gromacs in response to  
the equivalent acceleration?


Also I noticed that although in the .mdp file I specify:

; Non-equilibrium MD stuff
acc-grps = CH4
accelerate   = 0.0 0.0 -200.00

In the md.log file I get the following output

acc:0   0-154.549   0   0 45.4514

Can someone clarify what this means?

Any advice/comments appreciated



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[gmx-users] OPLS-AA: LJ problem? Atoms overlapping...

[Christopher Rowan]

Hello,

I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file.  My system topology I've
written by hand in an itp file.  The problem is that after any kind of run
the molecule penetrates the metal surface!  This shouldn't be happening.  I
had been using g45a3 quite successfully for the same system and everything
was working fine.  Do I need to do something different/special with oplsaa?
What am I missing?

Advice appreciated,
Chris Rowan
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[gmx-users] LINCS warnings with timestep of 5 fs (but not 4 fs)

[Chris Neale]

Hello,

I am recently experimenting with a 5 fs timestep using virtual hydrogens 
and LINCS. I am getting sporadic LINCS warnings, although the system 
appears stable and does not blow up during the 100ns in which I get such 
warnings. If I reduce the timestep to 4 fs from 5 fs (and increase 
nstlist to 5 from 4), then I do not get any such LINCS warnings. It 
occurs to me that in a larger timestep there could be a larger rotation 
and that this warning may be entirely benign. I am not sure about that, 
however, and would welcome any advice here, especially on the way that 
the 30 deg threshold for a warning message is derived.


Thank you,
Chris.


Here is a snippit from my stderr output during a run:

...
Step 1387503, time 6937.51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000156, max 0.001672 (between atoms 17832 and 17831)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 17832  17831   30.90.0946   0.0947  0.0945

Step 1387503, time 6937.51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000139, max 0.001582 (between atoms 17832 and 17828)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 17832  17831   31.10.0946   0.0946  0.0945

Step 3601434, time 18007.2 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.35, max 0.000308 (between atoms 18168 and 18165)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 18168  18167   30.10.0945   0.0945  0.0945

Step 4391822, time 21959.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000121, max 0.002041 (between atoms 14190 and 14189)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 14190  14189   30.50.0945   0.0947  0.0945

Step 4796357, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000128, max 0.001443 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 15532  15531   31.50.0945   0.0946  0.0945

Step 4796357, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000111, max 0.001185 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 15532  15531   31.80.0945   0.0946  0.0945

Step 4796358, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000221, max 0.002694 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 15532  15531   34.00.0946   0.0948  0.0945
...




With a .mdp file that looks like this:

integrator  =  sd
nsteps  =  2000
tinit   =  0
dt  =  0.005
comm_mode   =  linear
nstcomm =  4
comm_grps   =  System
nstxout =  2000
nstvout =  2000
nstfout =  2000
nstlog  =  0
nstlist =  4
nstenergy   =  2
nstxtcout   =  2
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
vdwtype =  cut-off
rvdw_switch =  0
rvdw=  1.4
rlist   =  0.9
DispCorr=  no
Pcoupl  =  Berendsen
pcoupltype  =  semiisotropic
compressibility =  4.5e-5 4.5e-5
ref_p   =  1. 1.
tau_p   =  4.04.0
tcoupl  =  Berendsen
tc_grps =  System
tau_t   =  1.0
ref_t   =  310.
ld-seed =  -1
annealing   =  no
gen_vel =  yes
unconstrained-start =  no
gen_temp=  310.
gen_seed=  -1
constraints =  all-bonds
constraint_algorithm=  lincs
lincs-iter  =  1
lincs-order =  6
;;;EOF


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[gmx-users] Huge acceleration needed to reproduce results!

[Chris Neale]

Gromacs uses nm as the unit of distance. Did you account for that? If so, please add some .mdp file 
snippits and any other relevant files so that we can see directly what you are doing.


Chris.

--- original message ---

Hello users,

I am trying to reproduce a calculation that I carried out in DL_POLY.  
It is to calculate the transport diffusion coefficient for CH4 in a  
frozen mesoporous silica.


In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per  
mole per angstrom). This equates to 10 dl_poly internal units which I  
add in this way at each timestep;


Fsum = Fsum + Fex

In Gromacs, I want to apply the same force as I used in DL_POLY so I  
calculated the required acceleration using F=ma. Where I took the mass  
to be the mass of one molecule of methane (16 a.m.u).


The final value for acceleration that I came up with (which  
corresponds to a force of 0.1kj mol-1 A-1 on each molecule) was 0.0625  
nm ps-2.


The first hiccup was when I used this value, the MSD was negative  
(though linear in the negative region of the graph). I assumed that  
this had something to do with the orientation of the unit cell and  
tried applying 0.0   0.0  -0.0625. The plot then looked much better.


The problem is when I calculate the Mean displacement of the CH4  
molecules. (I do this using a slightly altered version of the g_msd  
code). The Mean displacement  from gromacs is very different to that  
which I calculate using DL_POLY,


Gromacs gives 95.0, dl_poly 21347.0.

The MSD however (where I don?t add an acceleration are similar) so the  
problem lies with the force I am adding.


To test that it wasn?t some bug in my code to calculate the Mean  
displacement, I also looked at how the acceleration/force altered the  
MSD in DL_POLY and gromacs.


In DL_POLY, adding an external force of 0.1kj mol-1 A-1 would change  
the MSD of methane by 3 orders of magnitude compared to a run with no  
force added.


My equivalent acceleration of -0.0625 in gromacs, in comparison,  
barely changes the MSD from that of a run with no acceleration added.  
In fact it takes an acceleration of -200 in the z direction to cause  
such a difference in the Ds coefficients between runs with and without  
acceleration.


Does anyone have any idea what is going on here? An acceleration of  
200 ps nm-2 surely is not reasonable is it?. It seems very large  
compared to the example in the manual of 0.1. This would then imply  
that my back of the envelope calculation for relating force and  
acceleration is wrong. Am I missing something? I?m quite sure that the  
force I am adding in DL_POLY is equivalent to 0.1 kJ mol-1 A-1 so why  
are my methane molecules moving so much less in gromacs in response to  
the equivalent acceleration?


Also I noticed that although in the .mdp file I specify:

; Non-equilibrium MD stuff
acc-grps = CH4
accelerate   = 0.0 0.0 -200.00

In the md.log file I get the following output

acc:0   0-154.549   0   0 45.4514

Can someone clarify what this means?

Any advice/comments appreciated



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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[gmx-users] OPLS-AA: LJ problem? Atoms overlapping...

[Chris Neale]

Sounds like your topology/forcefield is incorrect or incomplete.

Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate 
that you don't have any LJ parameters for
some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters 
by hand. Are there any zero's where you should have numbers?
Perhaps you mixed up some atom types (e.g. with capitilization) or you simply 
didn't add the necessary values.

Chris.

-- original message --

Hello,

I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file.  My system topology I've
written by hand in an itp file.  The problem is that after any kind of run
the molecule penetrates the metal surface!  This shouldn't be happening.  I
had been using g45a3 quite successfully for the same system and everything
was working fine.  Do I need to do something different/special with oplsaa?
What am I missing?

Advice appreciated,
Chris Rowan

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[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

[Christopher Rowan]

Hi Chris,

I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.

Chris Rowan



Mon, 27 Jul 2009 12:30:54 -0700

Sounds like your topology/forcefield is incorrect or incomplete.

Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate
that you don't have any LJ parameters for
some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters
by hand. Are there any zero's where you should have numbers?
Perhaps you mixed up some atom types (e.g. with capitilization) or you simply
didn't add the necessary values.

Chris.

-- original message --

Hello,

I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file.  My system topology I've
written by hand in an itp file.  The problem is that after any kind of run
the molecule penetrates the metal surface!  This shouldn't be happening.  I
had been using g45a3 quite successfully for the same system and everything
was working fine.  Do I need to do something different/special with oplsaa?
What am I missing?

Advice appreciated,
Chris Rowan

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[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

[Chris Neale]

what's your minimum atomic distance achieved between Ag and your other molecule (g_mindist)? 


If it's < 0.09 nm then you definitely do have some error in your setup. For 
proof of that, generate a new system that is identical to yours
but this time use only standard OPLS atom-types and see the problem likely 
disapear.

If not, then the penetration is just because it goes between atoms and in this case, while you may not have an "error" per se, 
you should check your parameters and possibly your assumptions about what should be happening.


Also, it's very difficult to offer advice when you describe a problem without 
showing some of the important files directly.
Can you paste the changes to your .itp files and the ffopsaa.itp main file that 
you are using?

Hi Chris,

-- original message --

I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.

Chris Rowan



Mon, 27 Jul 2009 12:30:54 -0700

Sounds like your topology/forcefield is incorrect or incomplete.

Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate
that you don't have any LJ parameters for
some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters
by hand. Are there any zero's where you should have numbers?
Perhaps you mixed up some atom types (e.g. with capitilization) or you simply
didn't add the necessary values.

Chris.

-- original message --

Hello,

I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file.  My system topology I've
written by hand in an itp file.  The problem is that after any kind of run
the molecule penetrates the metal surface!  This shouldn't be happening.  I
had been using g45a3 quite successfully for the same system and everything
was working fine.  Do I need to do something different/special with oplsaa?
What am I missing?

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[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

[Christopher Rowan]

Here are some more details:

My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.

I could also add that each Ag belongs to its own charge group, so they
should be "felt".
I've tried starting with a different geometry as well with similar results.

Files were modified as follows:

ffoplsaa.atp  I added Silver as:

 AG107.87

ffoplsaanb.itp  I've added:

 AG AG 47   107.8700 0.000   A2.80455e-01  1.73304e-01

Chris Rowan
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[gmx-users] Segmentation Fault (Address not mapped)

[Darrell Koskinen]

Hi Justin,
With regard to your comment about using other force fields for my 
simulation of graphene surrounded by ammonia gas, are referring to the 
force fields for both graphene and ammonia or only to the force field 
for graphene?


I reviewed my selection of the force field parameters for graphene and 
see that I selected the parameters from the paper by Cornell et al. 
since a paper on deformation of carbon nanotubes ("A structural 
mechanics approach for the analysis of carbon nanotubes" by Chunyu Li, 
Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 
2487–2499) used parameters from the paper by Cornell et al. Is this 
sufficient to justify the use of these parameters? I also thought that 
graphene and ammonia would be considered organic since they are 
comprised of carbon, nitrogen, and hydrogen, which are all common 
elements found in organic matter.


With regard to the parameters for ammonia, is it acceptable to use the 
parameters from the paper by Cornell et al. or do I need to find papers 
specifically related to ammonia gas molecular dynamics simulations?


With regard to dihedral selection, I looked at the .top file and see 
that the function type is listed as 3 in the dihedrals section, which I 
believe indicates that my simulation is using a Ryckaert-Bellemans 
function. It appears to me that if I am using the OPLS force field that 
the Ryckaert-Bellemans dihedral type is automatically selected. I do see 
in the ffoplsaabon.itp file that there is an improper dihedral 
definition which think I could potentially use in my simulation 
"improper_Z_CA_X_Y", but how do I cause my simulation to use this 
definition? Do I need to add the following line to my .top file?

"#define improper_Z_CA_X_Y"

Further, I thought that I could simply modify the appropriate lines of 
the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found 
in the paper by Cornell et al. so that they will be used in my 
simulation. Am I correct in my assumption?


Thanks again for your help.

Darrell


>Date: Fri, 17 Jul 2009 22:11:07 -0400
>From: "Justin A. Lemkul" 
>Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>To: Discussion list for GROMACS users 
>Message-ID: <4a612f3b.7060...@vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>darre...@ece.ubc.ca wrote:
>> Hi Justin,
>> I am using the ffoplsaabon.itp parameters for:
>> bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3)
>> angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H)
>> dihedrals (X-CA-CA-X, X-CA-CT-X)
>>
>> I am using the ffolpsaanb.itp VdW parameters for H & N3
>>
>> And I am using the VdW parameters found in the paper "A Second
>> Generation Force Field for the Simulation of Proteins, Nucleic Acids,
>> and Organic Molecules" for CA, HA, CT, & HC doing the conversion from
>> Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from
>> kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. The
>> converted parameters for sigma were different by only +/-2% to +/-8%
>> from the values in ffoplsaanb.itp, but the converted parameters for
>> epsilon were different by +/-23% to +/-66% from the values in
>> ffoplsaanb.itp. Is this a valid paper to use for selection of 
parameters?

>>
>
>If memory serves, that paper is the derivation by Cornell, et al. for the
>AMBER94 parameter set, so no, you are not going to find those same 
parameters in

>ffoplsaanb.itp.
>
>Furthermore, the title of the paper indicates that the parameters are for
>proteins, nucleic acids, and organic molecules. Has anyone else in the
>literature used these parameters for graphene lattices? I would 
suggest using a
>force field that others have used for such solid materials, like 
nanotubes or
>other graphene surfaces. Otherwise, you will have to somehow 
demonstrate that a
>force field designed for use with condensed phase biomolecules is 
applicable to

>your gas-phase graphene lattice.
>
>> The graphene lattice is only vibrating slightly and looks like a 
bunch of

>> travelling waves.
>>
>> I believe I am using proper dihedrals and not improper dihedrals in my
>> model.
>>
>
>It would seem. Consider if impropers might be necessary to keep your 
planar

>groups planar. That's what they are there for.
>
>> Since the graphene structure will be connected to electrodes at both 
ends

>> and will be mounted above a substrate, I assume the atoms in the
>> structure are not completely free and thus I need to model them being
>> restricted in their movement. Maybe position restraints are more
>> appropriate than freezing to model such a situation.
>>
>> I do not see anything in the trajectory that provides clues as to what
>> might be causing the segmentation fault.
>>
>
>Then it will be very difficult to get any more remote help ;) If you
>consistently get the crash between step 20,000 and 30,000, then 
perhaps split
>your simulation into shorter sections, and during the time when you 
expect the
>crash to occu

[gmx-users] Fwd: fixed "3.3.3"?

[David Mobley]

All,

Is there any chance of getting an "official" patch released for 3.3.3  
that fixes the mdrun bug I have pointed out in the past, or perhaps an  
official, super-minor point release? I can provide the patch -- I'd  
just like it posted somewhere official.


The reason for this is that I'm trying to get some supercomputing  
folks to install the software system-wide, and they are reluctant to  
do it for my own "custom code" but I can probably get them to do it if  
it's an "official" patch.


I realize the developers are probably less than enthusiastic about  
doing anything further with 3.3.x. But I've got some free energy  
projects going in my own group and with some others that use tools  
that work only with 3.3.x, not 4.0.x. Additionally, we are reluctant  
to switch to 4.0.x without doing a lot of testing of the free energy  
components (which is yet another reason why we need a patched 3.3.x to  
compare to), given the number of times we were burned by free energy  
bugs in 3.3.x.


Thanks for your help.

David Mobley, Ph.D.
Assistant Professor of Chemistry
University of New Orleans
New Orleans, LA 70148
dlmob...@uno.edu
Office 504-280-6445
Fax 504-280-6860








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Re: [gmx-users] Segmentation Fault (Address not mapped)

[Justin A. Lemkul]

Darrell Koskinen wrote:

Hi Justin,
With regard to your comment about using other force fields for my 
simulation of graphene surrounded by ammonia gas, are referring to the 
force fields for both graphene and ammonia or only to the force field 
for graphene?




The "force field" should be one in the same.  The parameters should be suitably 
derived using the same scheme as the original work.


I reviewed my selection of the force field parameters for graphene and 
see that I selected the parameters from the paper by Cornell et al. 
since a paper on deformation of carbon nanotubes ("A structural 
mechanics approach for the analysis of carbon nanotubes" by Chunyu Li, 
Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 
2487–2499) used parameters from the paper by Cornell et al. Is this 
sufficient to justify the use of these parameters? I also thought that 
graphene and ammonia would be considered organic since they are 
comprised of carbon, nitrogen, and hydrogen, which are all common 
elements found in organic matter.




If you feel that precedent is sufficient, then I guess go ahead.  But realize 
that the paper by Cornell et al. refers to parameters suitable for simulations 
of proteins and nucleic acids, as well as a few organic functional groups. 
Parameterization was based on peptide backbone geometry, as well as other 
parameters, likely none of which involved graphene and gaseous ammonia (they 
were doing liquid simulations).


With regard to the parameters for ammonia, is it acceptable to use the 
parameters from the paper by Cornell et al. or do I need to find papers 
specifically related to ammonia gas molecular dynamics simulations?




I would seriously consider finding parameters (if they exist) that have been 
derived for use with gas-phase simulations.


With regard to dihedral selection, I looked at the .top file and see 
that the function type is listed as 3 in the dihedrals section, which I 
believe indicates that my simulation is using a Ryckaert-Bellemans 
function. It appears to me that if I am using the OPLS force field that 
the Ryckaert-Bellemans dihedral type is automatically selected. I do see 
in the ffoplsaabon.itp file that there is an improper dihedral 
definition which think I could potentially use in my simulation 
"improper_Z_CA_X_Y", but how do I cause my simulation to use this 
definition? Do I need to add the following line to my .top file?

"#define improper_Z_CA_X_Y"



No, you would have to use a special dihedrals section, that specifies the four 
atoms involved (function type 1), followed by the specification of that 
particular improper ("improper_Z_CA_X_Y").  See the manual for more details, 
and/or generate a topology for a protein with pdb2gmx with OPLS-AA and see how 
they're defined.


Further, I thought that I could simply modify the appropriate lines of 
the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found 
in the paper by Cornell et al. so that they will be used in my 
simulation. Am I correct in my assumption?




Modifying ffoplsaa files to parameters that are not OPLS-AA is probably a bad 
choice.  If you're dead-set on using these parameters, download the ffamber 
ports and use the ffamber94 force field, not some Frankensteined-OPLS.  Besides, 
all of the parameters in the Cornell paper are in kcal/mol/A^2, which will 
require conversion to Gromacs standard units.  If you've printed them directly 
in your previous attempts, I can guarantee you you're not getting the values you 
think you are.


-Justin


Thanks again for your help.

Darrell


 >Date: Fri, 17 Jul 2009 22:11:07 -0400
 >From: "Justin A. Lemkul" 
 >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
 >To: Discussion list for GROMACS users 
 >Message-ID: <4a612f3b.7060...@vt.edu>
 >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
 >
 >
 >
 >darre...@ece.ubc.ca wrote:
 >> Hi Justin,
 >> I am using the ffoplsaabon.itp parameters for:
 >> bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3)
 >> angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H)
 >> dihedrals (X-CA-CA-X, X-CA-CT-X)
 >>
 >> I am using the ffolpsaanb.itp VdW parameters for H & N3
 >>
 >> And I am using the VdW parameters found in the paper "A Second
 >> Generation Force Field for the Simulation of Proteins, Nucleic Acids,
 >> and Organic Molecules" for CA, HA, CT, & HC doing the conversion from
 >> Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from
 >> kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. 
The

 >> converted parameters for sigma were different by only +/-2% to +/-8%
 >> from the values in ffoplsaanb.itp, but the converted parameters for
 >> epsilon were different by +/-23% to +/-66% from the values in
 >> ffoplsaanb.itp. Is this a valid paper to use for selection of 
parameters?

 >>
 >
 >If memory serves, that paper is the derivation by Cornell, et al. for the
 >AMBER94 parameter set, so no, you are not going to find those sa

[gmx-users] Re: NH3 / graphene

[Paul Rowntree]

Darrell;

If memory serves, there was a paper in the late '80s of a simulation of 
monolayer NH3/graphite by William Steele.  It reproduced the lattice dimensions 
of our experiments, but seemed to over-estimate the corrugation in the binding 
energy relative to our diffraction experiments.

Hope this helps,

Paul Rowntree 
Dept. of Chemistry, University of Guelph 
 
> 
> Darrell Koskinen wrote:
> > Hi Justin,
> > With regard to your comment about using other force fields for my 
> > simulation of graphene surrounded by ammonia gas, are referring to
> the 
> > force fields for both graphene and ammonia or only to the force
> field 
> > for graphene?
> > 
> 
> The "force field" should be one in the same.  The parameters should be
> suitably 
> derived using the same scheme as the original work.
> 
> > I reviewed my selection of the force field parameters for graphene
> and 
> > see that I selected the parameters from the paper by Cornell et al.
> 
> > since a paper on deformation of carbon nanotubes ("A structural 
> > mechanics approach for the analysis of carbon nanotubes" by Chunyu
> Li, 
> > Tsu-Wei Chou in International Journal of Solids and Structures 40
> (2003) 
> > 2487�2499) used parameters from the paper by Cornell et al. Is this
> 
> > sufficient to justify the use of these parameters? I also thought
> that 
> > graphene and ammonia would be considered organic since they are 
> > comprised of carbon, nitrogen, and hydrogen, which are all common 
> > elements found in organic matter.
> > 
> 
> If you feel that precedent is sufficient, then I guess go ahead.  But
> realize 
> that the paper by Cornell et al. refers to parameters suitable for
> simulations 
> of proteins and nucleic acids, as well as a few organic functional
> groups. 
> Parameterization was based on peptide backbone geometry, as well as
> other 
> parameters, likely none of which involved graphene and gaseous ammonia
> (they 
> were doing liquid simulations).
> 
> > With regard to the parameters for ammonia, is it acceptable to use
> the 
> > parameters from the paper by Cornell et al. or do I need to find
> papers 
> > specifically related to ammonia gas molecular dynamics simulations?
> > 
> 
> I would seriously consider finding parameters (if they exist) that
> have been 
> derived for use with gas-phase simulations.
> 
> > With regard to dihedral selection, I looked at the .top file and see
> 
> > that the function type is listed as 3 in the dihedrals section,
> which I 
> > believe indicates that my simulation is using a Ryckaert-Bellemans 
> > function. It appears to me that if I am using the OPLS force field
> that 
> > the Ryckaert-Bellemans dihedral type is automatically selected. I do
> see 
> > in the ffoplsaabon.itp file that there is an improper dihedral 
> > definition which think I could potentially use in my simulation 
> > "improper_Z_CA_X_Y", but how do I cause my simulation to use this 
> > definition? Do I need to add the following line to my .top file?
> > "#define improper_Z_CA_X_Y"
> > 
> 
> No, you would have to use a special dihedrals section, that specifies
> the four 
> atoms involved (function type 1), followed by the specification of
> that 
> particular improper ("improper_Z_CA_X_Y").  See the manual for more
> details, 
> and/or generate a topology for a protein with pdb2gmx with OPLS-AA and
> see how 
> they're defined.
> 
> > Further, I thought that I could simply modify the appropriate lines
> of 
> > the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters
> found 
> > in the paper by Cornell et al. so that they will be used in my 
> > simulation. Am I correct in my assumption?
> > 
> 
> Modifying ffoplsaa files to parameters that are not OPLS-AA is
> probably a bad 
> choice.  If you're dead-set on using these parameters, download the
> ffamber 
> ports and use the ffamber94 force field, not some Frankensteined-OPLS.
>  Besides, 
> all of the parameters in the Cornell paper are in kcal/mol/A^2, which
> will 
> require conversion to Gromacs standard units.  If you've printed them
> directly 
> in your previous attempts, I can guarantee you you're not getting the
> values you 
> think you are.
> 
> -Justin
> 
> > Thanks again for your help.
> > 
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[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

[chris . neale]

What hydrogen did you use? Without substantially more cut and paste on  
your end I am in the dark and can't help very much.


On the side, I'll mention that your sigma, and especially your  
epsilon, looks very low here. I'm no gold expert though, and I am just  
pointing that out even though that is not likely to be the source of  
your problem.


 AG AG 47   107.8700 0.000   A2.80455e-01  1.73304e-01

I believe that I also asked for your ffoplsaa.itp file. Is your  
comb-rule set correctly? Are you sure that you are getting the  
ffoplsaanb.itp inclusion that you intend? For example, I use


...
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   3   yes 0.5 0.5

#include "/home/cneale/gromacs/oplspope.top/ffoplsaanb.itp"
#include "/home/cneale/gromacs/oplspope.top/ffoplsaabon.itp"
...

in my modified ffoplsaa.itp where the directories are hard coded to  
ensure that I get what I expect (rather than some unmodified  
ffoplsaanb.itp from $GMXLIB)


I can't think of anything else. You need to send a lot more data to  
this list. I am currently working under the assumption that you have  
made a mistake somewhere, and thus also assume that one of your  
descriptive statements is either misleading or incorrect -- hence the  
need for seeing the actual files (on list please). If, on the other  
hand, you are sure that you have done everything correctly then I  
can't help.


Good luck,
Chris

-- original message --

Here are some more details:

My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.

I could also add that each Ag belongs to its own charge group, so they
should be "felt".
I've tried starting with a different geometry as well with similar results.

Files were modified as follows:

ffoplsaa.atp  I added Silver as:

 AG107.87

ffoplsaanb.itp  I've added:

 AG AG 47   107.8700 0.000   A2.80455e-01  1.73304e-01

Chris Rowan


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Re: [gmx-users] POSITION-RESTRAIN

[Samik Bhattacharya]

--- On Mon, 27/7/09, Morteza Khabiri  wrote:

From: Morteza Khabiri 
Subject: [gmx-users] POSITION-RESTRAIN
To: gmx-users@gromacs.org
Date: Monday, 27 July, 2009, 7:35 PM

Dear gmxusers.

I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
             Atom index (53) in position_restraints out of bounds (1-52)
I found the similar error in the mailing list and they suggested probably
the place of restraint itp file which was included in  topology file is
wrong.  However, I tried several positions for restraint itp but I think
it is not the
solution. Do you have any other suggestion about this problem??

Thanks


hi, 
Mark is right.the position restrain.itp file should be included in your 
topology file in the proper place otherwise the problem would continue. place 
the .itp file after the section 
; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

best wishes 
Shamik

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[gmx-users] POSITION-RESTRAIN

[chris . neale]

Sounds to me like you have a 52 atom lipid and have a posre.itp file  
with more than 52 atoms (or referencing atom numbers greater than 52).  
What one usually does is has a somelipid.itp file that, upon some .mdp  
define, includes a someposre.itp file that looks like this:


[ position_restraints ]
; atom  type  fx  fy  fz
 8 1  1000  1000  1000

where for a 52 atom lipid I assume that you are using Berger lipids  
and atom 8 is the Phosphorous.


On the other hand, if you have a .itp file that specifies N-lipids,  
then you would need lots of [ position_restraints ]. Caution: this is  
not the best way to go as you will need to modify many files every  
time you set up a new bilayer.


As an analogy, look at the way that the SOL (tip4p in this case) posre  
is applied in a generic .top out of pdb2gmx:


#include "tip4p.itp"
#ifdef POSRES_SOL
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

where it is a per-molecule atomic index definition such that "atom 1"  
is applied to each solvent molecule.


If you are still unclear, I strongly suspect that there is a gmx  
manual description of all of this, and suggest that you read the  
manual in search of it. If you can't find one then probably you should  
complain back to this list about the absence of a section that should  
definitely be there.


Chris.

-- original message --

From: Morteza Khabiri 
Subject: [gmx-users] POSITION-RESTRAIN
To: gmx-users at gromacs.org
Date: Monday, 27 July, 2009, 7:35 PM

Dear gmxusers.

I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
 Atom index (53) in position_restraints out of bounds (1-52)
I found the similar error in the mailing list and they suggested probably
the place of restraint itp file which was included in  topology file is
wrong.  However, I tried several positions for restraint itp but I think
it is not the
solution. Do you have any other suggestion about this problem??

Thanks


hi,
Mark is right.the position restrain.itp file should be included in  
your topology file in the proper place otherwise the problem would  
continue. place the .itp file after the section

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

best wishes
Shamik



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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Mark Abraham]

Lee Soin wrote:

So there is no place to specify electrostatic interactions for pair
interactions?


No. The charges are specified in the [ atoms ] directive. Read the 
example in chapter 5.


Mark
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Re: [gmx-users] doubt - how to fix all atoms ?

[Mark Abraham]

Luis Paulo wrote:

Please

 I need  to fix all atoms of a proetin and I need to calculte the initital
enregy without to exceute septs of dynsmics.
How can i do this ?


Please start a fresh email when posting, lest search engines be confused 
by the contents of some other discussion.


You can do a zero-step energy minimization to calculate an energy. 
Fixing atoms would be irrelevant for that, and is a topic properly read 
about in the manual. Be aware that constraints, restraints and freeze 
groups are all distinct topics.


Mark
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[gmx-users] FeS cluster

[subarna thakur]

Hello
We dont have the parameters for Fe4S4 cluster in any of the the gomacs force 
fields but if we able to make the .itp file for the cluster manually with the 
help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in 
the include section of the  protein .top file later as done in the case of 
drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial 
for the Fe4S4 cluster?

With regards
Subarna


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Re: [gmx-users] FeS cluster

[Mark Abraham]

subarna thakur wrote:

Hello
We dont have the parameters for Fe4S4 cluster in any of the the gomacs force 
fields but if we able to make the .itp file for the cluster manually with the 
help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in 
the include section of the  protein .top file later as done in the case of 
drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial 
for the Fe4S4 cluster?


Yes and no. Even if you are able to obtain suitable parameters (which 
will be difficult at best), if there are bonded interactions to the 
cluster, then you will have to make a composite topology - i.e. a single 
[ moleculetype ]. Depending on the geometry and sequence order of your 
two chains, that might be painful too.


Frankly, this project would be a very poor one for a first effort at MD. 
Get some experience with GROMACS doing something more straightforward, 
learning to walk, before trying to run juggling razors.


Mark
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