[gmx-users] RE: Cut off problem

[Dallas Warren]

Are you running constant pressure?  If so, not surprising the box is shrinking, 
since it is a vacuum.  You should use constant volume.

Also, you cannot change the values of those settings you have within the .mdp 
unless you have a good reason to and/or it is allowable by the forcefield.  
These have particular values as defined by the forcefield, and you need to use 
those.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Anik Sen
Sent: Monday, 7 May 2012 2:55 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Cut off problem

Dear Gromacs users,

I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.
I want to see the interaction between some small atoms keeping them inside a 
periodic box without adding any solvent; i.e interaction between the atoms in 
the vacuum.
I have a total of 18-25 atoms in my system. The initial minimization was ok, 
but in case of the MD run, the job is failing after a few steps with the error,
Fatal error:
"One of the box vectors has become shorter than twice the cut off length or one 
of the box diagonal element has become smaller than cut off".
I have already changed the 'd' and 'rlist'; rvdw' and rcoulomb' to a number of 
different values to overcome the problem, but the problem persists.
How can I overcome this problem.

Thanking you in advance
Anik Sen

Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[Image removed by sender. www.csmcri.org]

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Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Mon, May 7, 2012 at 10:17 AM, Bala S  wrote:

> Justin and Anirban,
>
> I have another query on membrane simulation following your tutorials.
>
> How do I insert only a part of protein into the lipid bilayer and carryout
> the simulation?
>

editconf with -box option helps you to orient your protein with respect to
the bilayer. And visually in VMD you have the option of move a "molecule"
under "mouse" option in which you can move your protein wrt the bilayer
(when the bilayer and the protein .gro/.pdb files are loaded separately in
VMD).

-Anirban


>
> Thanks
> Bala S
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4957017.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Cut off problem

[Anik Sen]

Dear Gromacs users,

I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.
I want to see the interaction between some small atoms keeping them inside a 
periodic box without adding any solvent; i.e interaction between the atoms in 
the vacuum.
I have a total of 18-25 atoms in my system. The initial minimization was ok, 
but in case of the MD run, the job is failing after a few steps with the error,
Fatal error:
"One of the box vectors has become shorter than twice the cut off length or one 
of the box diagonal element has become smaller than cut off".
I have already changed the ‘d’ and ‘rlist’; rvdw’ and rcoulomb’ to a number of 
different values to overcome the problem, but the problem persists.
How can I overcome this problem.

Thanking you in advance
Anik Sen

Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]

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[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Bala S]

Justin and Anirban,

I have another query on membrane simulation following your tutorials.

How do I insert only a part of protein into the lipid bilayer and carryout
the simulation?

Thanks
Bala S

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4957017.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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RE: [gmx-users] the radius of dry core

[Dallas Warren]

RDF = probability function

Methylene density (number in the box (Nt) divided by the box volume), 
multiplied by probability (RDF) and shell volume (r+dr) calculates number of 
methylenes (Nm) within a given shell.

Fraction = Nm/Nt

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of dina dusti
Sent: Monday, 7 May 2012 2:05 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] the radius of dry core

Dear Dr. Warren,

Thank you very much from your help, but I want to calculate the fraction of 
methylenes in this distance to COM. How do I obtain this fraction in this 
distance by RDF, Please?

Thank you again.
Best Regards
Dina
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[gmx-users] the radius of dry core

[dina dusti]

Dear Dr. Warren,

Thank you very much from your help, but I want to calculate the fraction of 
methylenes in this distance to COM. How do I obtain this fraction in this 
distance by RDF, Please?

Thank you again.
Best Regards
Dina
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Re: [gmx-users] Topology parameters

[Shima Arasteh]

All right. 

Thank you so much.
Shima




 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Sunday, May 6, 2012 11:32 PM
Subject: Re: [gmx-users] Topology parameters
 


On 5/6/12 2:36 PM, Shima Arasteh wrote:
> IS the parameters for a residue in CHARMM36 and CHARMM27 the same?
>

I would suggest you do a bit of reading about the CHARMM force field hierarchy 
and why they are named as they are.  If you're parameterizing a new residue you 
can do it for either, or both, depending on the parameter set.  In your case, 
I'd suspect your formyl parameters are going to be universal between CHARMM27 
and CHARMM36, but don't let my suggestion be your justification.  If a reviewer 
asks, "some guy on the Internet said it" is not sufficient justification ;)

-Justin

> Thanks in advance,
> Shima
>
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Saturday, May 5, 2012 9:16 PM
> *Subject:* Re: [gmx-users] Topology parameters
>
>
>
> On 5/5/12 11:39 AM, Shima Arasteh wrote:
>  > Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and 
>CHARMM27?
>  >
>
> Maybe, try it and see. Swiss-Param might also be an option.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu  | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> -- gmx-users mailing list gmx-users@gromacs.org 
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>

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Positive potential energies for Dimethyl Aniline and Aniline

[Debayan Chakraborty]

Dear Justin,
   The Jorgensen group have already published results for
aniline and DMA using the OPLS-AA parameters. I am using the charges from
their publication ( R. Rizzo and W.L.Jorgensen, J.Am.Chem.Soc., 1994, 121,
4827-4836). Even after several crosschecks I have not been able to address
the problem.

Best,
Debayan

On Mon, May 7, 2012 at 12:31 AM, Justin A. Lemkul  wrote:

>
>
> On 5/6/12 11:42 AM, Debayan Chakraborty wrote:
>
>> Dear Colleagues,
>>   I am trying to build a well equilibrated
>> solvent box
>> of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I have
>> built
>> my topolgy files by closely following that given for 2-chloroaniline in
>> the
>> molecule and liquids database of virualchemistry.org
>> . I have even downloaded the files of
>> chloroaniline
>>
>> and ran short simulations. In those simulations I get negative potential
>> and
>> total energies, and even the Coulomb-recip term is negative.
>>
>> When I switch to my systems aniline and DMA, for both I get negative
>> potential
>> energies for the minimized structure. However, the coulomb-recip term is
>> positive in both cases. When I start my MD total energies for both
>> aniline and
>> DMA become positive, though aniline still retains a negative value of
>> potential
>> energy, the potential for DMA becomes positive.
>>
>> My questions are : Are positive or negative energies of a system during
>> simulation real indicators of something wrong in your MD ?
>>
>
> A positive potential indicates net repulsion.  In a normal,
> condensed-phase system, there should be net attraction.
>
>
>  How is it possible that chloroaniline,
>> aniline and
>> DMA which are closely related systems have so different values of
>> energies ?
>>
>
> "Closely related" is in the eye of the beholder.  Even small changes to
> chemical substituents can produce wildly different properties.  Yes, the
> molecules have the same general structure and "shape," but modifications of
> chemical groups can change the very nature of the molecule.  For instance,
> dimethylation of the amine on aniline removes its ability to form hydrogen
> bonds.
>
>
>  Does a positive Coulomb recip term indicate
>> wrong
>> representation of electrostatics ?
>>
>>
> Again this indicates net repulsion in the long-range electrostatic term
> (from PME).  It probably indicates that your model is not adequate, as the
> molecules are likely to be repelled from one another.
>
>
>  For all the systems I have used the charges from the OPLS-AA force field.
>> Any
>>
>
> How so?  If you're deriving parameters for a new topology, what exactly
> are you using?  Charges are not necessarily transferrable between
> molecules, though many common groups are.  Be careful what you interpret as
> "similar enough" if this is what you're doing.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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] How to build 1-4 pairs tables for -tablep in mdrun?

[Mark Abraham]

On 7/05/2012 5:50 AM, Marcelo Lopez wrote:

For sure, this wouldn't happened if the information to run all the
Gromacs features were clearly explained in the place where should be:
the manual.


Life would be good if everything was perfect, but when you're relying on 
free software provided by largely volunteer effort, you have to accept 
some imperfections.



Next time save some words and use your time to do a better
documentation job... unless you're trying to have some advantage...


You started these requests by asserting that no documentation existed. 
So various people who might have helped you were probably annoyed and 
decided not to give time to you. However, you got pointed to a likely 
source of information. You seem to have ignored that. Eventually I got 
bored of ignoring your repeated requests and pointed you in the right 
direction again. Others have made worthwhile suggestions, but as far as 
we know you're ignoring them, too. Your frustration with solving your 
problem is understandable, but your assumption that you are entitled to 
perfect free software and to abuse those who help produce it is not 
understandable.


Mark


Cheers!

2012/5/5 Mark Abraham:

On 5/05/2012 11:39 PM, Marcelo Lopez wrote:

Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:

How must I specify the 1-4 interaction in those tables? How many
columns and with what?


I suggested places to look for this information in answer to this question
more than a week ago.
http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html Your
reply addressed only another part of the discussion. Why are you asking the
same question again without appearing to have used the help you've been
given?



My primary goal is to set all the 1-4 interactions equal to zero. I
have some 1-4 pairs that aren't involved in dihedrals, that means that
setting up

nrexcl = 3

and

gen-pairs = no

isn't enough


In what sense? I suggested in that thread that you look at the contents of
the .log files to see if any Coulomb 1-4 interactions exist, but you've not
replied. Bald assertions that something doesn't work are likely to get
people who might help to assume that the most likely explanation is that
you're doing something wrong.

Mark

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RE: [gmx-users] the radius of dry core

[Dallas Warren]

Via the methylene - COM RDF.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of dina dusti
Sent: Sunday, 6 May 2012 3:42 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] the radius of dry core

Dear GROMACS Specialists,

I am working about micelles and have a question about the radius of dry core.
May I ask you to answer me, Please?
In one paper, I saw that the radius of dry core equals "where the density 
profiles of water and the surfactant hydrocarbon tails cross and a fraction of 
about 0.78 methylenes are found to be within this distance to COM".
I don't know how I obtain the fraction of methylenes in this distance to COM!
Please help me.

Thank you very much in advance.
Best Regards
Dina
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Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

[Justin A. Lemkul]

On 5/6/12 3:45 PM, Lara Bunte wrote:

Hi

You said:


The blank lines will be filled in with existing parameters from [angletypes] in 
ffbonded.itp.

I let the lines empty and I got an error at the first grompp, before energy 
minimization. grompp missed this empty lines. Here a part out of the errors:

ERROR 28 [file topol.top, line 229]:
   No default Angle types


ERROR 29 [file topol.top, line 233]:
   No default Improper Dih. types

My system is a cofactor, the force field is CHARMM27, parametrized with data 
out of a supporting information of a group that determined this parameters for 
my cofactor by experiments and quantum mechanical calculations. In 
residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave 
all informations (I guess).

What could be the problem?

I am able to complete the topol.top file by hand, but I really like to know 
what is the problem here.



A sequence of atoms in a topology (defined by atom type, not name or number) is 
mapped back to parameters in ffbonded.itp.  If no suitable parameters are found, 
you get the error messages.  In a normal topology (.top or .itp) for most force 
fields, the parameters are not explicitly stated because they are looked up in 
this manner.  If you're introducing something new or overriding existing force 
field parameters, you need to explicitly include them in the topology or add 
them to the appropriate directive in ffbonded.itp.


-Justin



Thanks for help

Greetings
Lara





- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 20:34 Dienstag, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology



Lara Bunte wrote:

Hi

In some lines the equilibrium angle and the force constant is missing.I give 
you an example:


The [ angles ] section is build like

[ angles ]
;  aiajak functc0c1c2c3
 2 119 1123.75 250.00
  1 23  1123.75 250.00
  1 24  1117.47 230.00



And my pdb2gmx output is for example something like

[ angles ]
;  aiajak functc0c1c2c3
  2 119 1123.75 250.00
  1 2 3  1
  1 2 4  1117.47 230.00




So you have a complete topology and one that has missing parameters, or are you 
adapting an incomplete topology?

What force field are you using?  What is the system?  For a normal protein system, most 
force fields (all except Gromos, if I recall) produce bonded directives with no 
parameters; they are looked up from ffbonded.itp and not stated explicitly, so 
"missing" parameters are completely normal and not problematic.  If you're 
dealing with something nonstandard and you've had to create .rtp entries, you'll need to 
post that information for diagnostic purposes.

In principle, there's nothing wrong with any of this.  The blank lines will be 
filled in with existing parameters from [angletypes] in ffbonded.itp.  These 
parameters are only overwritten if explicitly present in the topology.  If 
there is a bonded interaction referenced in the topology that does not exist in 
ffbonded.itp, grompp will fail with a fatal error.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] How to build 1-4 pairs tables for -tablep in mdrun?

[Marcelo Lopez]

For sure, this wouldn't happened if the information to run all the
Gromacs features were clearly explained in the place where should be:
the manual.
Next time save some words and use your time to do a better
documentation job... unless you're trying to have some advantage...
Cheers!

2012/5/5 Mark Abraham :
> On 5/05/2012 11:39 PM, Marcelo Lopez wrote:
>>
>> Hi, all, I'm still confused about how to set up 1-4 interaction tables
>> for tabulated non-bonding potentials when using the -tablep option in
>> mdrun.
>> The specific question is:
>>
>> How must I specify the 1-4 interaction in those tables? How many
>> columns and with what?
>
>
> I suggested places to look for this information in answer to this question
> more than a week ago.
> http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html Your
> reply addressed only another part of the discussion. Why are you asking the
> same question again without appearing to have used the help you've been
> given?
>
>
>> My primary goal is to set all the 1-4 interactions equal to zero. I
>> have some 1-4 pairs that aren't involved in dihedrals, that means that
>> setting up
>>
>> nrexcl = 3
>>
>> and
>>
>> gen-pairs = no
>>
>> isn't enough
>
>
> In what sense? I suggested in that thread that you look at the contents of
> the .log files to see if any Coulomb 1-4 interactions exist, but you've not
> replied. Bald assertions that something doesn't work are likely to get
> people who might help to assume that the most likely explanation is that
> you're doing something wrong.
>
> Mark
>
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Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

[Lara Bunte]

Hi

You said:

>The blank lines will be filled in with existing parameters from [angletypes] 
>in ffbonded.itp.
I let the lines empty and I got an error at the first grompp, before energy 
minimization. grompp missed this empty lines. Here a part out of the errors:

ERROR 28 [file topol.top, line 229]:
  No default Angle types


ERROR 29 [file topol.top, line 233]:
  No default Improper Dih. types

My system is a cofactor, the force field is CHARMM27, parametrized with data 
out of a supporting information of a group that determined this parameters for 
my cofactor by experiments and quantum mechanical calculations. In 
residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave 
all informations (I guess).

What could be the problem?

I am able to complete the topol.top file by hand, but I really like to know 
what is the problem here. 


Thanks for help

Greetings
Lara





- Ursprüngliche Message -
Von: Justin A. Lemkul 
An: Discussion list for GROMACS users 
CC: 
Gesendet: 20:34 Dienstag, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology



Lara Bunte wrote:
> Hi
> 
> In some lines the equilibrium angle and the force constant is missing.I give 
> you an example:
> 
> 
> The [ angles ] section is build like
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            
> c3
>    2     1    19     1    123.75     250.00
>     1     2    3      1    123.75     250.00
>     1     2    4      1    117.47     230.00
> 
> 
> 
> And my pdb2gmx output is for example something like
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            
> c3
>     2     1    19     1    123.75     250.00
>     1     2     3      1  
>     1     2     4      1    117.47     230.00
> 
> 

So you have a complete topology and one that has missing parameters, or are you 
adapting an incomplete topology?

What force field are you using?  What is the system?  For a normal protein 
system, most force fields (all except Gromos, if I recall) produce bonded 
directives with no parameters; they are looked up from ffbonded.itp and not 
stated explicitly, so "missing" parameters are completely normal and not 
problematic.  If you're dealing with something nonstandard and you've had to 
create .rtp entries, you'll need to post that information for diagnostic 
purposes.

In principle, there's nothing wrong with any of this.  The blank lines will be 
filled in with existing parameters from [angletypes] in ffbonded.itp.  These 
parameters are only overwritten if explicitly present in the topology.  If 
there is a bonded interaction referenced in the topology that does not exist in 
ffbonded.itp, grompp will fail with a fatal error.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Topology parameters

[Justin A. Lemkul]

On 5/6/12 2:36 PM, Shima Arasteh wrote:

IS the parameters for a residue in CHARMM36 and CHARMM27 the same?



I would suggest you do a bit of reading about the CHARMM force field hierarchy 
and why they are named as they are.  If you're parameterizing a new residue you 
can do it for either, or both, depending on the parameter set.  In your case, 
I'd suspect your formyl parameters are going to be universal between CHARMM27 
and CHARMM36, but don't let my suggestion be your justification.  If a reviewer 
asks, "some guy on the Internet said it" is not sufficient justification ;)


-Justin


Thanks in advance,
Shima


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, May 5, 2012 9:16 PM
*Subject:* Re: [gmx-users] Topology parameters



On 5/5/12 11:39 AM, Shima Arasteh wrote:
 > Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?
 >

Maybe, try it and see. Swiss-Param might also be an option.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Positive potential energies for Dimethyl Aniline and Aniline

[Justin A. Lemkul]

On 5/6/12 11:42 AM, Debayan Chakraborty wrote:

Dear Colleagues,
   I am trying to build a well equilibrated solvent box
of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I have built
my topolgy files by closely following that given for 2-chloroaniline in the
molecule and liquids database of virualchemistry.org
. I have even downloaded the files of chloroaniline
and ran short simulations. In those simulations I get negative potential and
total energies, and even the Coulomb-recip term is negative.

When I switch to my systems aniline and DMA, for both I get negative potential
energies for the minimized structure. However, the coulomb-recip term is
positive in both cases. When I start my MD total energies for both aniline and
DMA become positive, though aniline still retains a negative value of potential
energy, the potential for DMA becomes positive.

My questions are : Are positive or negative energies of a system during
simulation real indicators of something wrong in your MD ?


A positive potential indicates net repulsion.  In a normal, condensed-phase 
system, there should be net attraction.



 How is it possible that chloroaniline, aniline and
DMA which are closely related systems have so different values of energies ?


"Closely related" is in the eye of the beholder.  Even small changes to chemical 
substituents can produce wildly different properties.  Yes, the molecules have 
the same general structure and "shape," but modifications of chemical groups can 
change the very nature of the molecule.  For instance, dimethylation of the 
amine on aniline removes its ability to form hydrogen bonds.



 Does a positive Coulomb recip term indicate wrong
representation of electrostatics ?



Again this indicates net repulsion in the long-range electrostatic term (from 
PME).  It probably indicates that your model is not adequate, as the molecules 
are likely to be repelled from one another.



For all the systems I have used the charges from the OPLS-AA force field. Any


How so?  If you're deriving parameters for a new topology, what exactly are you 
using?  Charges are not necessarily transferrable between molecules, though many 
common groups are.  Be careful what you interpret as "similar enough" if this is 
what you're doing.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Topology parameters

[Shima Arasteh]

IS the parameters for a residue in CHARMM36 and CHARMM27 the same?

Thanks in advance,

Shima




 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Saturday, May 5, 2012 9:16 PM
Subject: Re: [gmx-users] Topology parameters
 


On 5/5/12 11:39 AM, Shima Arasteh wrote:
> Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?
> 

Maybe, try it and see.  Swiss-Param might also be an option.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Positive potential energies for Dimethyl Aniline and Aniline

[Debayan Chakraborty]

Dear Colleagues,
  I am trying to build a well equilibrated solvent
box of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I
have built my topolgy files by closely following that given for
2-chloroaniline in the molecule and liquids database of virualchemistry.org.
I have even downloaded the files of chloroaniline and ran short
simulations. In those simulations I get negative potential and total
energies, and even the Coulomb-recip term is negative.

When I switch to my systems aniline and DMA, for both I get negative
potential energies for the minimized structure. However, the coulomb-recip
term is positive in both cases. When I start my MD total energies for both
aniline and DMA become positive, though aniline still retains a negative
value of potential energy, the potential for DMA becomes positive.

My questions are : Are positive or negative energies of a system during
simulation real indicators of something wrong in your MD ?
How is it possible that chloroaniline, aniline
and DMA which are closely related systems have so different values of
energies ?
Does a positive Coulomb recip term indicate
wrong representation of electrostatics ?

For all the systems I have used the charges from the OPLS-AA force field.
Any help in this matter will be greatly appreciated. I have tried to think
hard about these issues but my limited knowledge about simulations have not
helped much

Best Regards,
Debayan Chakraborty
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Re: [gmx-users] Problem in GROMACS installation

[Mark Abraham]

On 6/05/2012 9:08 PM, amit banerjee wrote:

Dear Gromacs Users,
   I am trying to install gromacs 4.5.5 
version in a CENTOS 5.4 machine with FFTW 3.3.1.
To do so, I have downloaded both the tar.gz files in root and tried to 
install them as per the standard installation protocol.

Unfortunately i am receiving the following error.
/usr/bin/ld: /usr/local/lib/libfftw3f.a(apiplan.o): relocation 
R_X86_64_32 against `a local symbol' can not be used when making a 
shared object; recompile with -fPIC

/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/root/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1



See 
http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite


Mark
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[gmx-users] Problem in GROMACS installation

[amit banerjee]

Dear Gromacs Users,
   I am trying to install gromacs 4.5.5 version in 
a CENTOS 5.4 machine with FFTW 3.3.1.
To do so, I have downloaded both the tar.gz files in root and tried to install 
them as per the standard installation protocol.
Unfortunately i am receiving the following error.
/usr/bin/ld: /usr/local/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 
against `a local symbol' can not be used when making a shared object; recompile 
with -fPIC
/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/root/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1


Seeking your support to solve the issue.
Looking forward for your solutions.

Thanks and regards,
Amit K Banerjee

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