[gmx-users] Are there some environment variables not valid anymore?

[Theodore Si]

Hi,

I find this in the installation instruction part GMX 5.0：


 Helping CMake find the right libraries/headers/programs
 

If libraries are installed in non-default locations their location can 
be specified using the following environment variables:


 * |CMAKE_INCLUDE_PATH|for header files
 * |CMAKE_LIBRARY_PATH|for libraries
 * |CMAKE_PREFIX_PATH|for header, libraries and binaries
   (e.g.|/usr/local|).



However when I set the CMAKE_INCLUDE_PATH with -DCMAKE_INCLUDE_PATH I 
get this:


 209 //No help, variable specified on the command line.
 210 
CMAKE_INCLUDE_PATH:UNINITIALIZED=/home/theo/myprg/vt/include/vampirtrace/


Why?

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[gmx-users] Charmm to gromacs

[Abu Naser]

Hi All,

I took the following from Mark's script to convert non-bonded parameters of ZN 
manually:

printf("% 5s %f   0.0 A %.4g %.4g\n", $atom, $element_mass, 2*$four_epsilon 
* $sigma**6, $four_epsilon * $sigma**12); 


I am getting:

-0.0002245 -1.205e-08

instead of:

0.194215920555  1.046


Am I missing anything? 

I would appreciate your respond. 


With regards,

Abu 







  
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[gmx-users] How to use Gromacs toolkit to analyse streaming velocity profile in NEMD

[Junfang.Zhang]

Dear Gromacs users
Could you let me know how to use Gromacs toolkit to analyse streaming velocity 
profile (average velocity in a channel direction, x,  as a function of 
specified box vector z, vx (z)) in non-equilibrium molecular dynamics 
simulation.
Regards
Junfang





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gromacs.org_gmx-users@maillist.sys.kth.se

[Theodore Si]

Hi,

Can we set the number manually with -npme when using GPU acceleration?


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[gmx-users] Positive potential energy during Energy minimization step

[neha bharti]

I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.

After Adding Ion

genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

I preform energy minimization step. In energy minimization step I am
getting possitive potential enargy:

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  6.1499341e+17
Maximum force =inf on atom 3300
Norm of force =  5.4206209e+18


its mention in the tutorial verify that the values of Epot and Fmax are
reasonable before continuing

I am trying alot but not able to fix the issue.

Its mention in tutorial but I am not able to find the exactly what to do.

please help.

With Regards
Neha bharty
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[gmx-users] can we use AMBER12 FF?

[Albert]

Hello:


I am just wondering can we use Amber12 FF in Gromacs now?

thank you very much

Albert
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Re: [gmx-users] ligand binding

[Justin Lemkul]

On 8/7/14, 8:47 AM, Meenakshi Rajput wrote:

Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin


There are no hard and fast rules when running normal MD simulations.


protein complex? As for emtol=1000, complex(mentioned in the tutorial) is
converged in some steps and graph plotted for potential energy shows sudden
downfall. Please tell me what is the reason behind this?



If there is a dramatic decrease in energy, there should be an obvious structural 
change somewhere.  Watch the trajectory.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

[Justin Lemkul]

On 8/7/14, 2:00 PM, Steven Morgan wrote:

I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG 
repeated five times.  I am trying to calculate entropy and the eigenvalues of 
the covariance matrix to get eigenfrequencies.  When I issue the command gmx 
covar -f full.trr -s full.tpr -v -o -mwa (for eigenvalues), I get an empty 
eigenvalues.xvg.  In GROMACS v4.5.5 I used to get the eigenvalues outputted, 
for the same data sets, same command (g_covar).  It says it's writing the 
eigenvalues, but when I open the file there are no eigenvalues there, only the 
preamble for the xvg file, ending at @TYPE xy.  What am I doing wrong or is 
this a bug?



Sounds like a bug.  Please file an issue on redmine.gromacs.org and upload 
example input files that reproduce the problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] New residue in FF does not bond to others.

[Justin Lemkul]

The problem is in atom naming.  You have used MN1 and MC3 for the equivalent of 
amino acid N and C atoms, respectively.  pdb2gmx chokes here, because Phe-65 
tries to make a bond to the +N atom, which it does not find until it runs into 
Ser-69.  Likewise with the C atom in CH6.  If you rename these atoms (MN1->N, 
MC3->C) in the .rtp and .hdb, everything works fine.


If there are still missing parameters for interactions, you'll have to figure 
that out.  There are several missing inter-residue angles and dihedrals in your 
.rtp entry for CH6.


-Justin

On 8/7/14, 11:48 AM, Dawid das wrote:

http://www.speedyshare.com/9EhEf/charm27-files.tar.bz2
http://www.speedyshare.com/AMWM7/mCherry7.tar.bz2

Like I said they are the same except two extra lines in aminoacids.rtp file.


2014-08-07 2:27 GMT+01:00 Justin Lemkul :




On 8/6/14, 1:36 PM, Dawid das wrote:


These are lines that cause trouble:

ERROR 1 [file mCherry7.top, line 18183]:
No default U-B types


ERROR 2 [file mCherry7.top, line 18250]:
No default U-B types


ERROR 3 [file mCherry7.top, line 25379]:
No default Proper Dih. types


ERROR 4 [file mCherry7.top, line 25380]:
No default Proper Dih. types


ERROR 5 [file mCherry7.top, line 25383]:
No default Proper Dih. types


ERROR 6 [file mCherry7.top, line 25386]:
No default Proper Dih. types


ERROR 7 [file mCherry7.top, line 25387]:
No default Proper Dih. types


ERROR 8 [file mCherry7.top, line 25388]:
No default Proper Dih. types


ERROR 9 [file mCherry7.top, line 25455]:
No default Proper Dih. types


ERROR 10 [file mCherry7.top, line 25457]:
No default Proper Dih. types

ERROR 11 [file mCherry7.top, line 25458]:
No default Proper Dih. types

   Now in these files which I have already uploaded I have only added two
extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp
(lines 1793 and 1794):
  MC3 +N  0.1345  154808.0
  MN1 -C  0.139   173594.2

I have not changed anything else in any other file.
Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1
atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6
is
supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not
supposed
to be bonded to NH1 atom of Ser69 but it is in my *top file. What other
files do you need?



The same ones you provided before.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Charmm to gromacs

[Justin Lemkul]

On 8/8/14, 3:11 AM, Abu Naser wrote:

Hi All,

I took the following from Mark's script to convert non-bonded parameters of ZN 
manually:

printf("% 5s %f   0.0 A %.4g %.4g\n", $atom, $element_mass, 2*$four_epsilon 
* $sigma**6, $four_epsilon * $sigma**12);


I am getting:

-0.0002245 -1.205e-08

instead of:

0.194215920555  1.046


Am I missing anything?

I would appreciate your respond.



Probably something wrong with your input file.  There's no need to do these 
conversions; we provide the latest CHARMM36 FF for Gromacs at 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Positive potential energy during Energy minimization step

[Justin Lemkul]

On 8/8/14, 7:25 AM, neha bharti wrote:

I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.

After Adding Ion

genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

I preform energy minimization step. In energy minimization step I am
getting possitive potential enargy:

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  6.1499341e+17
Maximum force =inf on atom 3300
Norm of force =  5.4206209e+18


its mention in the tutorial verify that the values of Epot and Fmax are
reasonable before continuing

I am trying alot but not able to fix the issue.

Its mention in tutorial but I am not able to find the exactly what to do.



You have infinite force, so you have unresolvable atomic clashes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Are there some environment variables not valid anymore?

[Justin Lemkul]

On 8/8/14, 1:22 AM, Theodore Si wrote:

Hi,

I find this in the installation instruction part GMX 5.0：


  Helping CMake find the right libraries/headers/programs
  

If libraries are installed in non-default locations their location can be
specified using the following environment variables:

  * |CMAKE_INCLUDE_PATH|for header files
  * |CMAKE_LIBRARY_PATH|for libraries
  * |CMAKE_PREFIX_PATH|for header, libraries and binaries
(e.g.|/usr/local|).



However when I set the CMAKE_INCLUDE_PATH with -DCMAKE_INCLUDE_PATH I get this:

  209 //No help, variable specified on the command line.
  210 CMAKE_INCLUDE_PATH:UNINITIALIZED=/home/theo/myprg/vt/include/vampirtrace/

Why?



The wiki is out of date.  CMAKE_PREFIX_PATH still works, but the other two do 
not.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] New residue in FF does not bond to others.

[Dawid das]

2014-08-08 15:48 GMT+01:00 Justin Lemkul :

> The problem is in atom naming.  You have used MN1 and MC3 for the
> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes here,
> because Phe-65 tries to make a bond to the +N atom, which it does not find
> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you rename
> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.
>

OK, I see your point but if I do as you suggest how will I specify
nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
atoms have different  vdW and electrostatic parameters than N and C atoms,
respectively.



> If there are still missing parameters for interactions, you'll have to
> figure that out.  There are several missing inter-residue angles and
> dihedrals in your .rtp entry for CH6.
>

Do you mean those which I stated above?
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Re: [gmx-users] New residue in FF does not bond to others.

[Justin Lemkul]

On 8/8/14, 12:39 PM, Dawid das wrote:

2014-08-08 15:48 GMT+01:00 Justin Lemkul :


The problem is in atom naming.  You have used MN1 and MC3 for the
equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes here,
because Phe-65 tries to make a bond to the +N atom, which it does not find
until it runs into Ser-69.  Likewise with the C atom in CH6.  If you rename
these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.



OK, I see your point but if I do as you suggest how will I specify
nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
atoms have different  vdW and electrostatic parameters than N and C atoms,
respectively.



Realize that atom *names* and atom *types* are separate entities.  You have all 
your names and types the same, which can be confusing.  All you need to do is 
*name* the atom N and assign it a *type* of MNH1 or whatever it was.  Parameters 
are always assigned by type, not name.






If there are still missing parameters for interactions, you'll have to
figure that out.  There are several missing inter-residue angles and
dihedrals in your .rtp entry for CH6.



Do you mean those which I stated above?



Above?  You mean in a previous message?  Most of those errors were derived from 
incorrect, nonsensical bonding.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] New residue in FF does not bond to others.

[Dawid das]

Thank you but now I have different type of question.
If I use -nocmap option for pdb2gmx what impact on the result of my
simulation?


2014-08-08 19:42 GMT+01:00 Justin Lemkul :

>
>
> On 8/8/14, 12:39 PM, Dawid das wrote:
>
>> 2014-08-08 15:48 GMT+01:00 Justin Lemkul :
>>
>>  The problem is in atom naming.  You have used MN1 and MC3 for the
>>> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes
>>> here,
>>> because Phe-65 tries to make a bond to the +N atom, which it does not
>>> find
>>> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you
>>> rename
>>> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.
>>>
>>>
>> OK, I see your point but if I do as you suggest how will I specify
>> nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
>> atoms have different  vdW and electrostatic parameters than N and C atoms,
>> respectively.
>>
>>
> Realize that atom *names* and atom *types* are separate entities.  You
> have all your names and types the same, which can be confusing.  All you
> need to do is *name* the atom N and assign it a *type* of MNH1 or whatever
> it was.  Parameters are always assigned by type, not name.
>
>
>
>>
>>  If there are still missing parameters for interactions, you'll have to
>>> figure that out.  There are several missing inter-residue angles and
>>> dihedrals in your .rtp entry for CH6.
>>>
>>>
>> Do you mean those which I stated above?
>>
>>
> Above?  You mean in a previous message?  Most of those errors were derived
> from incorrect, nonsensical bonding.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] New residue in FF does not bond to others.

[Justin Lemkul]

On 8/8/14, 1:58 PM, Dawid das wrote:

Thank you but now I have different type of question.
If I use -nocmap option for pdb2gmx what impact on the result of my
simulation?



Then you won't have CMAP terms, i.e. you'll basically be reverting back to the 
old CHARMM22 force field.


-Justin



2014-08-08 19:42 GMT+01:00 Justin Lemkul :




On 8/8/14, 12:39 PM, Dawid das wrote:


2014-08-08 15:48 GMT+01:00 Justin Lemkul :

  The problem is in atom naming.  You have used MN1 and MC3 for the

equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes
here,
because Phe-65 tries to make a bond to the +N atom, which it does not
find
until it runs into Ser-69.  Likewise with the C atom in CH6.  If you
rename
these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.



OK, I see your point but if I do as you suggest how will I specify
nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
atoms have different  vdW and electrostatic parameters than N and C atoms,
respectively.



Realize that atom *names* and atom *types* are separate entities.  You
have all your names and types the same, which can be confusing.  All you
need to do is *name* the atom N and assign it a *type* of MNH1 or whatever
it was.  Parameters are always assigned by type, not name.





  If there are still missing parameters for interactions, you'll have to

figure that out.  There are several missing inter-residue angles and
dihedrals in your .rtp entry for CH6.



Do you mean those which I stated above?



Above?  You mean in a previous message?  Most of those errors were derived
from incorrect, nonsensical bonding.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] New residue in FF does not bond to others.

[Dawid das]

Very well. Thank you for your assistance :).


2014-08-08 21:00 GMT+01:00 Justin Lemkul :

>
>
> On 8/8/14, 1:58 PM, Dawid das wrote:
>
>> Thank you but now I have different type of question.
>> If I use -nocmap option for pdb2gmx what impact on the result of my
>> simulation?
>>
>>
> Then you won't have CMAP terms, i.e. you'll basically be reverting back to
> the old CHARMM22 force field.
>
> -Justin
>
>
>
>> 2014-08-08 19:42 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 8/8/14, 12:39 PM, Dawid das wrote:
>>>
>>>  2014-08-08 15:48 GMT+01:00 Justin Lemkul :

   The problem is in atom naming.  You have used MN1 and MC3 for the

> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes
> here,
> because Phe-65 tries to make a bond to the +N atom, which it does not
> find
> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you
> rename
> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works
> fine.
>
>
>  OK, I see your point but if I do as you suggest how will I specify
 nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and
 MC3
 atoms have different  vdW and electrostatic parameters than N and C
 atoms,
 respectively.


  Realize that atom *names* and atom *types* are separate entities.  You
>>> have all your names and types the same, which can be confusing.  All you
>>> need to do is *name* the atom N and assign it a *type* of MNH1 or
>>> whatever
>>> it was.  Parameters are always assigned by type, not name.
>>>
>>>
>>>
>>>
   If there are still missing parameters for interactions, you'll have to

> figure that out.  There are several missing inter-residue angles and
> dihedrals in your .rtp entry for CH6.
>
>
>  Do you mean those which I stated above?


  Above?  You mean in a previous message?  Most of those errors were
>>> derived
>>> from incorrect, nonsensical bonding.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
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>>> Gromacs Users mailing list
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>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

[Tsjerk Wassenaar]

Hi Steven,

The eigenvalue is the variance of the projection over time. So in stead of
waiting for the bug fix, you can also calculate the projections and get the
eigenvalues from those.

Hope it helps,

Tsjerk
On Aug 7, 2014 10:32 PM, "Steven Morgan"  wrote:

> I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG
> repeated five times.  I am trying to calculate entropy and the eigenvalues
> of the covariance matrix to get eigenfrequencies.  When I issue the command
> gmx covar -f full.trr -s full.tpr -v -o -mwa (for eigenvalues), I get an
> empty eigenvalues.xvg.  In GROMACS v4.5.5 I used to get the eigenvalues
> outputted, for the same data sets, same command (g_covar).  It says it's
> writing the eigenvalues, but when I open the file there are no eigenvalues
> there, only the preamble for the xvg file, ending at @TYPE xy.  What am I
> doing wrong or is this a bug?
>
> Thank you,
> -Steven
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[gmx-users] g_wham cycl or periodic

[ANDRES ADOLFO ORTEGA GUERRERO]

Hi Dear Gromacs User,

I was wondering if you could help me explaing something, i usea g_wham for
a PMF calculation of a molecule passing through an ion channel, i use the
option cycl and periodic, i think the cycl is the right choice?, but i dont
understand the concept of if my calculations are periodic or cyclic. Could
you help me with this.

Thanks, Andrés
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Re: [gmx-users] g_wham cycl or periodic

[Justin Lemkul]

On 8/8/14, 2:41 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:

Hi Dear Gromacs User,

I was wondering if you could help me explaing something, i usea g_wham for
a PMF calculation of a molecule passing through an ion channel, i use the
option cycl and periodic, i think the cycl is the right choice?, but i dont
understand the concept of if my calculations are periodic or cyclic. Could
you help me with this.



The use of -cycl implies that the free energy at the minimum and maximum value 
of the reaction coordinate is the same.  Your situation should qualify, because 
your molecule will have (theoretically) zero interaction at long distances away 
from the channel on either side of it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Lysozyme-Water Tutorial problem : em.tpr

[Agnivo Gosai]

Dear Users

I have been following the Lysozyme in Water tutorial by Dr. Lemkul step by
step (GROMACS Version 4.6.5) and I must confess that I am a beginner.

I am now stuck in Step 5 : Energy Minimization.
I had performed the step :-

*grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
*

Next when I proceeded with : -

*mdrun -v -deffnm em*

I got the following message in my terminal :-







*Program mdrun, VERSION 4.6.5Source code file:
/build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524Can not open
file:-em.tprFor more information and tips for troubleshooting, please
check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
*
-

I am not sure as to how to carry on to the next level. Any insight is
very much appreciated.


Best Regards,

Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University
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Re: [gmx-users] Lysozyme-Water Tutorial problem : em.tpr

[Justin Lemkul]

On 8/8/14, 2:53 PM, Agnivo Gosai wrote:

Dear Users

I have been following the Lysozyme in Water tutorial by Dr. Lemkul step by
step (GROMACS Version 4.6.5) and I must confess that I am a beginner.

I am now stuck in Step 5 : Energy Minimization.
I had performed the step :-

*grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
*

Next when I proceeded with : -

*mdrun -v -deffnm em*

I got the following message in my terminal :-







*Program mdrun, VERSION 4.6.5Source code file:
/build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524Can not open
file:-em.tprFor more information and tips for troubleshooting, please
check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
*
-

I am not sure as to how to carry on to the next level. Any insight is
very much appreciated.



If it's looking for a file called "-em.tpr" then you haven't typed your mdrun 
command correctly.  This error won't come up if you type the command exactly as 
shown in the tutorial.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Nose-Hoover + Parrinello Rahman reduces density of liquid phase as compared to Berendsen thermostat + barostat

[Mark Abraham]

We can't tell without more information - at least your GROMACS version,
.mdp settings and the length of time over which you collected
post-equilibration data.

Mark


On Thu, Aug 7, 2014 at 9:50 PM, Yip Yew Mun  wrote:

> Hi, I ran a simulation of 1-octanol in liquid phase and I discovered that
> when i ran production simulations with Nose-Hoover thermostat + Parrinello
> Rahman barostat, the density deviates by about 34 kg/m^3 from the
> experimental value, which using the Berendsen thermostat + barostat, the
> density is well-maintained. I’m using the opals forcefield. Therefore, I
> wish to ask if this is normal, and if it is not, what can I do to rectify
> it?
>
> Thanks.
>
> Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> Biological Chemistry
> School of Physical & Mathematical Sciences | Nanyang Technological
> University | Singapore 639798
> Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h
>
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gromacs.org_gmx-users@maillist.sys.kth.se

[Mark Abraham]

You can set the number of PME-only ranks with -npme. Whether it's useful is
another matter :-) The CPU-based PME offload and the GPU-based PP offload
do not combine very well.

Mark


On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si  wrote:

> Hi,
>
> Can we set the number manually with -npme when using GPU acceleration?
>
>
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Re: [gmx-users] can we use AMBER12 FF?

[Mark Abraham]

You can find the supported force fields in share/gromacs/top, and they do
not include AMBER12

Mark


On Fri, Aug 8, 2014 at 8:44 AM, Albert  wrote:

> Hello:
>
>
> I am just wondering can we use Amber12 FF in Gromacs now?
>
> thank you very much
>
> Albert
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Re: [gmx-users] Charmm to gromacs

[Abu Naser]

Thanks Justin for your response. 

I just manually inserted the input values only to that part of the script.  The 
atom types I am interested in, they are not available in the charmm36. Since I 
have only few unusual atom types, I wish to do them manually and trying to 
figure out how it can be converted. 







 

> Date: Fri, 8 Aug 2014 08:50:16 -0600
> From: jalem...@vt.edu
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
> 
> 
> 
> On 8/8/14, 3:11 AM, Abu Naser wrote:
> > Hi All,
> >
> > I took the following from Mark's script to convert non-bonded parameters of 
> > ZN manually:
> >
> > printf("% 5s %f   0.0 A %.4g %.4g\n", $atom, $element_mass, 
> > 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12);
> >
> >
> > I am getting:
> >
> > -0.0002245 -1.205e-08
> >
> > instead of:
> >
> > 0.194215920555  1.046
> >
> >
> > Am I missing anything?
> >
> > I would appreciate your respond.
> >
> 
> Probably something wrong with your input file.  There's no need to do these 
> conversions; we provide the latest CHARMM36 FF for Gromacs at 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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[gmx-users] Can I delete trr file?

[Batdorj Batsaikhan]

Dear gmx users,

I am new user of gromacs. Our calculations are running, but we have a problem 
that has not enough disk space. Therefore I need to delete some file that are 
unimportant for analysis. Is there any analysis use trr file? Can I delete trr 
file?


Best regards, 

Batsaikhan
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