Re: [gmx-users] (no subject)

[Sanim Rahman]

Hi Justin,

I completely dazed over the "download .tgz" option at the top right of the
screen. I got all of the files I need for my membrane. Thank you!

*Sanim Rahman*


On Sat, Mar 18, 2017 at 8:03 AM, Justin Lemkul  wrote:

>
>
> On 3/18/17 1:25 AM, Sanim Rahman wrote:
>
>> Sorry I found this thread here:
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2016-September/108197.html
>>
>>
>> From my understanding, I use pdb2gmx on my entire output file, however,
>> where does the data in the .psf file go?
>>
>>
> You shouldn't be using pdb2gmx at all.  CHARMM-GUI gives you a complete
> system topology that should work, as long as you don't modify anything
> about the system.
>
> -Justin
>
>
> *Sanim Rahman*
>> B.S. Chemical Engineering, 2019
>> Resident Assistant, Castor Hall Engineering Living Learning Community
>> 2016-2017
>> Co-Founder and Co-President of the Undergraduate Research Society
>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>> 
>>
>>
>> On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman 
>> wrote:
>>
>> Hi all,
>>>
>>> I am trying to run grompp on POPC lipid bilayer that I constructed in
>>> CHARMM-GUI. I originally input the whole assembled bilayer from
>>> CHARMM-GUI,
>>> however, I received the error:
>>>
>>> "No Default U-B Types"
>>>
>>> From a few previous threads, it was suggested that I stripped the waters
>>> and use pdb2gmx on them separately in GROMACS. I did that and included
>>> the
>>> #include command in my lipid topology file to reference water.itp.
>>> However,
>>> I receive the following error:
>>>
>>> "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr
>>> =
>>> 1,
>>> while at->nr = 17152)"
>>>
>>> This is what the end of my POPC topology file looks like:
>>>
>>> *; Include Position restraint file*
>>> *#ifdef POSRES*
>>> *#include "posre.itp"*
>>> *#endif*
>>>
>>> *; Include water chain topology*
>>> *#include "water.itp"*
>>>
>>> *; Include water topology*
>>> *#include "./charmm36-nov2016.ff/tip3p.itp"*
>>>
>>> *#ifdef POSRES_WATER*
>>> *; Position restraint for each water oxygen*
>>> *[ position_restraints ]*
>>> *;  i funct   fcxfcyfcz*
>>> *   11   1000   1000   1000*
>>> *#endif*
>>>
>>> *; Include topology for ions*
>>> *#include "./charmm36-nov2016.ff/ions.itp"*
>>>
>>> *[ system ]*
>>> *; Name*
>>> *Protein*
>>>
>>> *[ molecules ]*
>>> *; Compound#mols*
>>> *Other   1*
>>> *Water   1*
>>>
>>> I recalled implementing the same technique in one of the GROMACS
>>> tutorials,
>>> but I am unsure what I am doing differently in my approach to receive
>>> this
>>> error.
>>> Thank you. I will truly appreciate your assistance.
>>> *Sanim Rahman*
>>> B.S. Chemical Engineering, 2019
>>> Resident Assistant, Castor Hall Engineering Living Learning Community
>>> 2016-2017
>>> Co-Founder and Co-President of the Undergraduate Research Society
>>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>>> 
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pressure problem in EM simulation

[Mark Abraham]

Hi,

You haven't done a simulation, you've moved down a potential energy surface
from one point to another. Of course the potential energy deviates. How
much depends how far away from something reasonable you were when you
started :-)

Mark

On Sun, Mar 19, 2017 at 2:19 AM Mishelle Oña  wrote:

> Thanks for your answer Justin.
>
> Another question for the same simulation. I got this values of potential
> energy:
>
> Average> -127776
>
> Err.Est.>4900
>
> RMSD>12891.3
>
> Tot-Drift> -32877.9
>
> I think the RMSD is way too high. What do you think?
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: Saturday, March 18, 2017 8:06 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Pressure problem in EM simulation
>
>
>
> On 3/18/17 9:00 PM, Mishelle Oña wrote:
> > Hello!
> >
> > I have a question about pressure in EM simulation. I am using Steepest
> descent method in a water polymer system. My pressure gets this value:
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> ---
> > Pressure   -2843.38 65162.655   -446.059
> (bar)
> >
> > The pressure value is very weird. Is this normal? or I am doing
> something wrong?
> >
>
> There's no barostat or velocities during EM so the value you see has no
> real
> significance.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> http://mackerell.umaryland.edu/~jalemkul>
>
> Justin A. Lemkul - MacKerell Lab
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please
> use the navigation links above.
>
>
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> GMX-Users List - Gromacs<
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
> www.gromacs.org
> This is the main discussion forum for users of GROMACS and related
> software. Subscribe, unsubscribe or change your preferences through
> gmx-users Admin page.
>
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Mailing Lists - Gromacs
> www.gromacs.org
> The three mailing lists (see the menu items on the left) have slightly
> different purposes, and you might not be interested in subscribing to all
> of them:
>
>
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> gromacs.org_gmx-users Info Page - Royal Institute of ...<
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> maillist.sys.kth.se
> gromacs.org_gmx-users -- Discussion list for GROMACS users About
> gromacs.org_gmx-users
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pressure problem in EM simulation

[Justin Lemkul]

On 3/18/17 9:18 PM, Mishelle Oña wrote:

Thanks for your answer Justin.

Another question for the same simulation. I got this values of potential energy:

Average> -127776

Err.Est.>4900

RMSD>12891.3

Tot-Drift> -32877.9

I think the RMSD is way too high. What do you think?



Consider the name "energy minimization" and then plot the energy as a function 
of step.  Does it make sense to try to obtain average statistics during a 
process designed to dramatically alter the energy?


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Saturday, March 18, 2017 8:06 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure problem in EM simulation



On 3/18/17 9:00 PM, Mishelle Oña wrote:

Hello!

I have a question about pressure in EM simulation. I am using Steepest descent 
method in a water polymer system. My pressure gets this value:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -2843.38 65162.655   -446.059  (bar)

The pressure value is very weird. Is this normal? or I am doing something wrong?



There's no barostat or velocities during EM so the value you see has no real
significance.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.



==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - 
Gromacs
www.gromacs.org
This is the main discussion forum for users of GROMACS and related software. 
Subscribe, unsubscribe or change your preferences through gmx-users Admin page.



* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Mailing Lists - Gromacs
www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly 
different purposes, and you might not be interested in subscribing to all of 
them:



* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
gromacs.org_gmx-users Info Page - Royal Institute of 
...
maillist.sys.kth.se
gromacs.org_gmx-users -- Discussion list for GROMACS users About 
gromacs.org_gmx-users




--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pressure problem in EM simulation

[Mishelle Oña]

Thanks for your answer Justin.

Another question for the same simulation. I got this values of potential energy:

Average> -127776

Err.Est.>4900

RMSD>12891.3

Tot-Drift> -32877.9

I think the RMSD is way too high. What do you think?


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Saturday, March 18, 2017 8:06 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure problem in EM simulation



On 3/18/17 9:00 PM, Mishelle Oña wrote:
> Hello!
>
> I have a question about pressure in EM simulation. I am using Steepest 
> descent method in a water polymer system. My pressure gets this value:
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Pressure   -2843.38 65162.655   -446.059  (bar)
>
> The pressure value is very weird. Is this normal? or I am doing something 
> wrong?
>

There's no barostat or velocities during EM so the value you see has no real
significance.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.



==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - 
Gromacs
www.gromacs.org
This is the main discussion forum for users of GROMACS and related software. 
Subscribe, unsubscribe or change your preferences through gmx-users Admin page.



* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Mailing Lists - Gromacs
www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly 
different purposes, and you might not be interested in subscribing to all of 
them:



* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
gromacs.org_gmx-users Info Page - Royal Institute of 
...
maillist.sys.kth.se
gromacs.org_gmx-users -- Discussion list for GROMACS users About 
gromacs.org_gmx-users


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pressure problem in EM simulation

[Justin Lemkul]

On 3/18/17 9:00 PM, Mishelle Oña wrote:

Hello!

I have a question about pressure in EM simulation. I am using Steepest descent 
method in a water polymer system. My pressure gets this value:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -2843.38 65162.655   -446.059  (bar)

The pressure value is very weird. Is this normal? or I am doing something wrong?



There's no barostat or velocities during EM so the value you see has no real 
significance.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Pressure problem in EM simulation

[Mishelle Oña]

Hello!

I have a question about pressure in EM simulation. I am using Steepest descent 
method in a water polymer system. My pressure gets this value:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -2843.38 65162.655   -446.059  (bar)

The pressure value is very weird. Is this normal? or I am doing something wrong?

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Surface tension/pressure calculation

[Merril Mathew]

Dear all,

I would like to calculate surface tension/pressure of my monolayer
simulation. I have two monolayers of lipid each side of a water box. So
four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I
used NVT simulation. Is there a way to calculate surface tension/pressure
of lipid/water in my system using GROMACS tools?

I used: gmx energy to get #Surf*SurfTens. What does this do?
Is it possible to calculate the surface tension of my monolayers using the
formula:

 [image: Inline images 1]
I can get Pzz, Pxx and Pyy for my system from gmx_energy. Is Lz the box
size in Z direction, i.e normal to my monolayer in nanometers? If I solve
this equation does the value mean the average surface tension of my
monolayers?

Thanks,
Merril.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Doubt from force constant calculations

[Justin Lemkul]

On 3/18/17 7:36 AM, Rakesh Pant wrote:

Dear Justin,

Could you briefly tell how the vibrational analysis is done. Which method
and software is generally used.



The primary literature for the chosen force field should have this information.

-Justin


Thanks
Rakesh

On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul  wrote:




On 3/17/17 7:53 AM, Rakesh Pant wrote:


Dear all,

How to calculate force constant for bonds and angles using quantum
chemistry calculations.



Typically a vibrational analysis is done and force constants are set to
reproduce the frequencies.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] MDRUN doesn't print Hessian Matrix as ordered

[Justin Lemkul]

On 3/18/17 6:46 AM, Juan José Galano Frutos wrote:

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:

* Thank you Justin for your replay. I've read that to compute specific

*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool calculates such a correction using the Hessian matrix.
*>* Is for that reason my interest in getting it.
*>* So, my question is why mdrun is not producing the indicated Hessian
*>* matrix as set up in the command line. What I am missing, maybe in the
*>* .mdp file??
*>
And I asked you about the contents of the .mdp file, which you haven't
provided.
  Are you setting "integrator = nm" in it?

-Justin

Sorry Justin. As you can see below I'm using an md integrator. Then,
if I'm understanding well it is possible to obtain the required
Hessian matrix only when you perform normal modes simulations..?



Yes, I believe so.


If so, I have another question because although I've been reading a
lot about this quantum correction issue to exactly determine specific
heats I am not yet so clear about this:

What about the printing frequency of energy in this kind of analysis?
Is it really necessary set the higher frequency of printing energy as
possible in order to get good accuracy in this calculation or it is
not certainly so important?



Sorry, no idea.  I've never done such calculations.  Hopefully someone who has 
will chime in.


-Justin


Thanks again for your help.

;
;   juanjo (2016)
;
title   = md_prod
cpp = /lib/cpp
define  =

integrator  = md
dt  = 0.002 ; ps !
nsteps  = 100   ; total 2 ns.
nstcomm = 1
nstxtcout   = 25000 ; each 50 ps.
xtc-precision   = 25000
nstxout = 25000 ; each 50 ps.
nstvout = 25000
nstfout = 25000
nstlog  = 1000
nstenergy   = 1000


 >* Thank
*>>>* On 3/17/17 8:20 AM, Juan José Galano Frutos wrote:
*>>* * Hi there:
*>* *>>* I am trying to calculate the specific heat (Cp) of my
protein, but I should
*>* *>* take into account quantum correction as indicated lately.
Then, I need to
*>* *>* obtain from the production step the Hessian Matrix including the
*>* *>* eigenvectors needed to calculate the vibrational energy.
*>* *>* So, the point is that I set in my script the following order:
*>* *>>* mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
*>* *>* ${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
*>* *>* ${NAME}-hessian.mtx -nice 19 -v
*>* *>>* and in fact, the program apparently recognizes well that a
Hessian matrix
*>* *>* should be printed (see -mtx option below), but however I do
not get such a
*>* *>* Hessian matrix at the end. What's happening here then? I've been looking
*>* *>* for any related discussion online, or whether I have to set
any additional
*>* *>* option, maybe in the mdp file to obtain the Hesssian matrix but I've not
*>* *>* achieved it.
*>* *
*>* What's in your .mdp file?  IIRC the Hessian is only relevant when
doing normal
*>* modes analysis.
*>>* -Justin
*>>>* * Any help, please.
*>* *>>* Thank you very much in advance.
*>* *>>>*  :-)  G  R  O  M  A  C  S  (-:
*>* *>>*  Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*>* *>>* :-)  VERSION 4.6.1  (-:
*>* *>>* Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
*>* *>*Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
*>* *>*  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof,
Christoph Junghans,
*>* *>* Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
*>* *>*Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
*>* *>* Michael Shirts, Alfons Sijbers, Peter Tieleman,
*>* *>>*Berk Hess, David van der Spoel, and Erik Lindahl.
*>* *>>*Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
*>* *>*  Copyright (c) 2001-2012,2013, The GROMACS development team at
*>* *>* Uppsala University & The Royal Institute of Technology, Sweden.
*>* *>* check out http://www.gromacs.org 
*>* > for more information.
*>* *>>*  This program is free software; you can redistribute it and/or
*>* *>*modify it under the terms of the GNU Lesser General
Public License
*>* *>* as published by the Free Software Foundation; either version 2.1
*>* *>*  of the License, or (at your option) any later version.
*>* *>>*   :-)  mdrun_mpi  (-:
*>* *>>* Option Filename  Type Description
*>* *>* 
*>* *>*   -s folded-2ns.tpr  InputRun input file: tpr tpb tpa
*>* *>*   -o folded-2ns.trr  Output   Full precision 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 3/18/17 1:25 AM, Sanim Rahman wrote:

Sorry I found this thread here:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html


From my understanding, I use pdb2gmx on my entire output file, however,
where does the data in the .psf file go?



You shouldn't be using pdb2gmx at all.  CHARMM-GUI gives you a complete system 
topology that should work, as long as you don't modify anything about the system.


-Justin


*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research



On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman  wrote:


Hi all,

I am trying to run grompp on POPC lipid bilayer that I constructed in
CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI,
however, I received the error:

"No Default U-B Types"

From a few previous threads, it was suggested that I stripped the waters
and use pdb2gmx on them separately in GROMACS. I did that and included the
#include command in my lipid topology file to reference water.itp. However,
I receive the following error:

"Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
1,
while at->nr = 17152)"

This is what the end of my POPC topology file looks like:

*; Include Position restraint file*
*#ifdef POSRES*
*#include "posre.itp"*
*#endif*

*; Include water chain topology*
*#include "water.itp"*

*; Include water topology*
*#include "./charmm36-nov2016.ff/tip3p.itp"*

*#ifdef POSRES_WATER*
*; Position restraint for each water oxygen*
*[ position_restraints ]*
*;  i funct   fcxfcyfcz*
*   11   1000   1000   1000*
*#endif*

*; Include topology for ions*
*#include "./charmm36-nov2016.ff/ions.itp"*

*[ system ]*
*; Name*
*Protein*

*[ molecules ]*
*; Compound#mols*
*Other   1*
*Water   1*

I recalled implementing the same technique in one of the GROMACS tutorials,
but I am unsure what I am doing differently in my approach to receive this
error.
Thank you. I will truly appreciate your assistance.
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] protein-ligand complex mdrun errors

[Justin Lemkul]

On 3/17/17 12:43 PM, Vignesh Waran wrote:

respected sir,

  i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?

my command line   gmx mdrun -v -deffnm em


how to find the clarify the problem?
 pls tell me sir


GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em

*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*

Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this
machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*



This suggests that you're linking against the wrong version of a library.  How 
did you install GROMACS (what was your exact cmake command)? And what does ldd 
tell you about the libraries to which mdrun is linked?


-Justin



bioinformatics@bioinformatics-desktop:~/Desktop/Gromacs$ ls
em.mdp mdout.mdp  RET.pdb  RLBP_solv_ions.gro  topol.top
complex.gro  em.tpr #mdout.mdp.1#  RLBP1.grosolv.gro
 #topol.top.1#
drg.itp  ions.tpr   minim.mdp  RLBP1.pdb#temp.topRLSaIL.1#
 #topol.top.2#
em.log   JZ4 model  posre.itp  RLBP_newbox.gro  #temp.topW9R5zG.1#

this file run the energy minimization







--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Doubt from force constant calculations

[Rakesh Pant]

Dear Justin,

Could you briefly tell how the vibrational analysis is done. Which method
and software is generally used.

Thanks
Rakesh

On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul  wrote:

>
>
> On 3/17/17 7:53 AM, Rakesh Pant wrote:
>
>> Dear all,
>>
>> How to calculate force constant for bonds and angles using quantum
>> chemistry calculations.
>>
>>
> Typically a vibrational analysis is done and force constants are set to
> reproduce the frequencies.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

[Juan José Galano Frutos]

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:
>* Thank you Justin for your replay. I've read that to compute specific
*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool calculates such a correction using the Hessian matrix.
*>* Is for that reason my interest in getting it.
*>* So, my question is why mdrun is not producing the indicated Hessian
*>* matrix as set up in the command line. What I am missing, maybe in the
*>* .mdp file??
*>
And I asked you about the contents of the .mdp file, which you haven't
provided.
  Are you setting "integrator = nm" in it?

-Justin

Sorry Justin. As you can see below I'm using an md integrator. Then,
if I'm understanding well it is possible to obtain the required
Hessian matrix only when you perform normal modes simulations..?

If so, I have another question because although I've been reading a
lot about this quantum correction issue to exactly determine specific
heats I am not yet so clear about this:

What about the printing frequency of energy in this kind of analysis?
Is it really necessary set the higher frequency of printing energy as
possible in order to get good accuracy in this calculation or it is
not certainly so important?

Thanks again for your help.

;
;   juanjo (2016)
;
title   = md_prod
cpp = /lib/cpp
define  =

integrator  = md
dt  = 0.002 ; ps !
nsteps  = 100   ; total 2 ns.
nstcomm = 1
nstxtcout   = 25000 ; each 50 ps.
xtc-precision   = 25000
nstxout = 25000 ; each 50 ps.
nstvout = 25000
nstfout = 25000
nstlog  = 1000
nstenergy   = 1000


 >* Thank
*>>>* On 3/17/17 8:20 AM, Juan José Galano Frutos wrote:
*>>* * Hi there:
*>* *>>* I am trying to calculate the specific heat (Cp) of my
protein, but I should
*>* *>* take into account quantum correction as indicated lately.
Then, I need to
*>* *>* obtain from the production step the Hessian Matrix including the
*>* *>* eigenvectors needed to calculate the vibrational energy.
*>* *>* So, the point is that I set in my script the following order:
*>* *>>* mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
*>* *>* ${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
*>* *>* ${NAME}-hessian.mtx -nice 19 -v
*>* *>>* and in fact, the program apparently recognizes well that a
Hessian matrix
*>* *>* should be printed (see -mtx option below), but however I do
not get such a
*>* *>* Hessian matrix at the end. What's happening here then? I've been looking
*>* *>* for any related discussion online, or whether I have to set
any additional
*>* *>* option, maybe in the mdp file to obtain the Hesssian matrix but I've not
*>* *>* achieved it.
*>* *
*>* What's in your .mdp file?  IIRC the Hessian is only relevant when
doing normal
*>* modes analysis.
*>>* -Justin
*>>>* * Any help, please.
*>* *>>* Thank you very much in advance.
*>* *>>>*  :-)  G  R  O  M  A  C  S  (-:
*>* *>>*  Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*>* *>>* :-)  VERSION 4.6.1  (-:
*>* *>>* Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
*>* *>*Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
*>* *>*  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof,
Christoph Junghans,
*>* *>* Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
*>* *>*Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
*>* *>* Michael Shirts, Alfons Sijbers, Peter Tieleman,
*>* *>>*Berk Hess, David van der Spoel, and Erik Lindahl.
*>* *>>*Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
*>* *>*  Copyright (c) 2001-2012,2013, The GROMACS development team at
*>* *>* Uppsala University & The Royal Institute of Technology, Sweden.
*>* *>* check out http://www.gromacs.org 
*>* > for more information.
*>* *>>*  This program is free software; you can redistribute it and/or
*>* *>*modify it under the terms of the GNU Lesser General
Public License
*>* *>* as published by the Free Software Foundation; either version 2.1
*>* *>*  of the License, or (at your option) any later version.
*>* *>>*   :-)  mdrun_mpi  (-:
*>* *>>* Option Filename  Type Description
*>* *>* 
*>* *>*   -s folded-2ns.tpr  InputRun input file: tpr tpb tpa
*>* *>*   -o folded-2ns.trr  Output   Full precision trajectory: trr trj cpt
*>* *>*   -x folded-2ns.xtc  Output, Opt! Compressed trajectory (portable xdr
*>* *>* format)
*>* *>* -cpi  state.cpt  Input, Opt.  Checkpoint file
*>* *>* -cpo  

[gmx-users] Dihedral restraint in explicit water

[Anurag Kumar]

Dear all,

Restraining dihedral for dipeptide in explicit water model, how it can be
done?

Thank you,
Anurag Kumar
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] protein-ligand complex mdrun errors

[Vignesh Waran]

espected sir,

  i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?

my command line   gmx mdrun -v -deffnm em


how to find the clarify the problem?
 pls tell me sir


GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em

*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*

Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this
machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*


bioinformatics@bioinformatics-desktop:~/Desktop/Gromacs$ ls
em.mdp mdout.mdp  RET.pdb  RLBP_solv_ions.gro  topol.top
complex.gro  em.tpr #mdout.mdp.1#  RLBP1.grosolv.gro
 #topol.top.1#
drg.itp  ions.tpr   minim.mdp  RLBP1.pdb#temp.topRLSaIL.1#
 #topol.top.2#
em.log   JZ4 model  posre.itp  RLBP_newbox.gro  #temp.topW9R5zG.1#

this file run the energy minimization


-- 
Regards,
T. Vigneshnwaran,
M.Tech final year Bioinformatics,
Bharathidasan University,
Trichy, Tamilnadu, India.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] protein-ligand complex mdrun errors

[Vignesh Waran]

espected sir,

  i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?

my command line   gmx mdrun -v -deffnm em


how to find the clarify the problem?
 pls tell me sir


GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em

*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*

Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this
machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
*ymbol lookup error: gmx: undefined symbol: getFilenm---this my problem sir*


bioinformatics@bioinformatics-desktop:~/Desktop/Gromacs$ ls
em.mdp mdout.mdp  RET.pdb  RLBP_solv_ions.gro  topol.top
complex.gro  em.tpr #mdout.mdp.1#  RLBP1.grosolv.gro
 #topol.top.1#
drg.itp  ions.tpr   minim.mdp  RLBP1.pdb#temp.topRLSaIL.1#
 #topol.top.2#
em.log   JZ4 model  posre.itp  RLBP_newbox.gro  #temp.topW9R5zG.1#

this file run the energy minimization


-- 
Regards,
T. Vigneshnwaran,
M.Tech final year Bioinformatics,
Bharathidasan University,
Trichy, Tamilnadu, India.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.