[gmx-users] Counter-ion in a initially neutral system

[Alex]

Dear gromacs user,

In my simulation (solid surface + peptide in aqueous solution) I have a
heptpeptide in which contains 2 times Glutamic acid (negatively charged)
and one Arginine(positively charge) and one Lysine(positively charge), so,
as you see the heptpeptide is charge neutral in general(the whole system is
also neutral) despite having charged amino acid.
However, In such situation I see sometimes people add also "Na + Cl" as
counter-ion in the system, I do not know why!, I was wondering if it is
really necessary to do that or make sense, as It is neutral initially?
What if I do not add them?
How can I see their effects quantitatively?
How can I find out if I need the Counter-ions or not?

By, the way, the goal of simulation is to calculate the PMF of
heptapeptide-surface interaction* in *physiological condition by US.

Thanks in advance.
Regards,
Alex
-- 
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] Issues with huge system

[Kevin Chen]

Hi Gromacs Users,

 

We 've observed  some issues while creating huge simulation boxes (over35
nm* 35 nm * 35nm in size). Commands used for building our benchmarks showed
as follow:

gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -box 33 33 33 -bt
cubic

gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr

gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 8

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

The problem only showed up when using box size greater than 30nm * 30nm * 30
nm. Once the box is bigger than 30*30*30, the simulation always crashes
during EM stage. However everything is fine when using any box sizes smaller
than 30*30*30.   As such, we are eager to know if that was something we did
wrong or there's some sort of issues for Gromacs dealing with large systems.
Any suggestions and pointers are welcome!

Thanks in advance,

Kevin

-- 
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] qm/mm LA not found

[Sylwia Kacprzak]

Dear all,

I have set qm/mm calculations with Gromacs 5.1.4 and Orca.
I treat first the full cofactor on a QM level. However when I cut the 
bond to take only part of it for QM and
introduce link atom according to the manual with link atom (LA) I get 
following error.


---
Program gmx grompp, VERSION 5.1.4
Source code file: 
/home/widu/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line: 1345


Fatal error:
Atomtype LA not found

Any ideas?

Greetings
Sylwia

--
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] Questions about free energy calculation tutorial

[gozde ergin]

Thank Justin, ok I understand now. 
Then I need to run the simulation with +1 charge, since I made 0 of all the 
charges in SDS, Na+ charge will stay there.
Do you think it is ok run with +1 charge?

> On 04 Nov 2016, at 13:36, Justin Lemkul  wrote:
> 
> No, you should not.  The topology you posted before had Na+ as part of the 
> SDS [moleculetype] and you were decoupling the whole thing.  This is what I 
> am saying you should not be doing if you're trying to get just the hydration 
> free energy of SDS.
> 
> -Justin

-- 
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] Questions about free energy calculation tutorial

[Justin Lemkul]

On 11/4/16 8:34 AM, gozde ergin wrote:

If you want the hydration free energy of SDS, you should not include Na+ 
because the simultaneous decoupling will include the hydration free energy of 
Na+.  You can subtract that out, but there is error associated with that 
calculation and accounting for that is not necessarily easy.  It is 
straightforward to just deal with SDS alone.


Yes this is exactly what I want but I did not get how the Na+ would be included 
simultaneously?
My SDS.itp file contains C12H25SO4- molecules, Na+ is not inside this file. 
There is another SOD.itp file that contains Na+.
So if I only write SDS to couple-moltype in .mdp file, it will decouple 
C12H25SO4- but not Na+.
Should I put Na+ atom inside the SDS.itp?



No, you should not.  The topology you posted before had Na+ as part of the SDS 
[moleculetype] and you were decoupling the whole thing.  This is what I am 
saying you should not be doing if you're trying to get just the hydration free 
energy of SDS.


-Justin


On 04 Nov 2016, at 12:51, Justin Lemkul  wrote:



On 11/3/16 10:56 AM, gozde ergin wrote:

You can decouple atomic and molecular ions, there are just additional 
considerations like an interface potential to calculate.  See, e.g. work by 
Benoit Roux.


Yes I can but do I need to? I just want to know the free energy of solvation of 
SDS. If I do not include the Na ion decoupling, is it wrong?



I

-Justin


On 02 Nov 2016, at 12:42, Justin Lemkul  wrote:



On 11/1/16 9:02 AM, gozde ergin wrote:

This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


If I do not include the Na ion in decoupling I do not have this warning.
If I do not decouple Na ion still I need to make the charge of this molecule 
zero otherwise system charge becomes +1.


Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.


My purpose is doing the same thing with SDS that you did with Methane. And as 
SDS has Na ion I thought I need also to decouple it.
Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
Last question even if I do not decouple the Na ion I need to make it charge 
zero, right?



You can decouple atomic and molecular ions, there are just additional 
considerations like an interface potential to calculate.  See, e.g. work by 
Benoit Roux.

-Justin


Thanks in advance.

On 01 Nov 2016, at 13:21, Justin Lemkul  wrote:



On 11/1/16 7:31 AM, gozde ergin wrote:

Hi Justin,

I would like to ask one question related to this tutorial. I do the same thing 
with using SDS (Sodium dodecyl sulfate) molecule.
As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate part. 
However in order to estimate the free energy of SDS salvation in water I need 
to decouple the all SDS molecule. Since couple-moltype accept only one types of 
molecule, I hacked the topology and put all atoms I want to decouple in the 
same [moleculetype] :

[ moleculetype ]
; name  nrexcl
SDS  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
  1 SL  1  SDS  S  1  0.00032.0600   ; qtot  
1.330
  2OSL  1  SDSOS1  2  0.00015.9994   ; qtot  
1.050
  3O2L  1  SDSOS2  3  0.00015.9994   ; qtot  
0.400
  4O2L  1  SDSOS3  4  0.00015.9994   ; qtot 
-0.250
  5O2L  1  SDSOS4  5  0.00015.9994   ; qtot 
-0.900
   .
   .
 25   HAL2  1  SDSH71 25  0.000 1.0080   ; qtot 
-1.090
 26   HAL2  1  SDSH72 26  0.000 1.0080   ; qtot 
-1.000
 27   CTL2  1  SDS C8 27  0.00012.0110   ; qtot 
-1.180
  .
  .
 42   HAL3  1  SDS   H123 42  0.000 1.0080   ; qtot 
-1.000
 43SOD  2  SDSSOD 43  0.00022.9898   ; qtot  
1.000
.

However I get this warning during the simulation :

WARNING: Listed nonbonded interaction between particles 25 and 43
at distance 2.303 which is larger than the table limit 2.200 nm.

Do you have any idea how could I get rid off this warning?



This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


Also does the hacked .top file seem correct?



Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences 

Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

> If you want the hydration free energy of SDS, you should not include Na+ 
> because the simultaneous decoupling will include the hydration free energy of 
> Na+.  You can subtract that out, but there is error associated with that 
> calculation and accounting for that is not necessarily easy.  It is 
> straightforward to just deal with SDS alone.

Yes this is exactly what I want but I did not get how the Na+ would be included 
simultaneously? 
My SDS.itp file contains C12H25SO4- molecules, Na+ is not inside this file. 
There is another SOD.itp file that contains Na+. 
So if I only write SDS to couple-moltype in .mdp file, it will decouple 
C12H25SO4- but not Na+. 
Should I put Na+ atom inside the SDS.itp?

> On 04 Nov 2016, at 12:51, Justin Lemkul  wrote:
> 
> 
> 
> On 11/3/16 10:56 AM, gozde ergin wrote:
>>> You can decouple atomic and molecular ions, there are just additional 
>>> considerations like an interface potential to calculate.  See, e.g. work by 
>>> Benoit Roux.
>> 
>> Yes I can but do I need to? I just want to know the free energy of solvation 
>> of SDS. If I do not include the Na ion decoupling, is it wrong?
>> 
> 
> I
> 
> -Justin
> 
>>> On 02 Nov 2016, at 12:42, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 11/1/16 9:02 AM, gozde ergin wrote:
>> This is a generic simulation failure message, indicating that your 
>> system is blowing up.  This could be due to any number of reasons, but 
>> without more details it's pointless to guess.
 
 If I do not include the Na ion in decoupling I do not have this warning.
 If I do not decouple Na ion still I need to make the charge of this 
 molecule zero otherwise system charge becomes +1.
 
>> Decoupling the Na+ ion will mean your resulting dG value includes the 
>> hydration free energy of Na+, which it doesn't sound like you're 
>> interested in.
 
 My purpose is doing the same thing with SDS that you did with Methane. And 
 as SDS has Na ion I thought I need also to decouple it.
 Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
 Last question even if I do not decouple the Na ion I need to make it 
 charge zero, right?
 
>>> 
>>> You can decouple atomic and molecular ions, there are just additional 
>>> considerations like an interface potential to calculate.  See, e.g. work by 
>>> Benoit Roux.
>>> 
>>> -Justin
>>> 
 Thanks in advance.
> On 01 Nov 2016, at 13:21, Justin Lemkul  wrote:
> 
> 
> 
> On 11/1/16 7:31 AM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I would like to ask one question related to this tutorial. I do the same 
>> thing with using SDS (Sodium dodecyl sulfate) molecule.
>> As you know there is NA (Sodium) atom that not bonded to dodecyl 
>> sulphate part. However in order to estimate the free energy of SDS 
>> salvation in water I need to decouple the all SDS molecule. Since 
>> couple-moltype accept only one types of molecule, I hacked the topology 
>> and put all atoms I want to decouple in the same [moleculetype] :
>> 
>> [ moleculetype ]
>> ; name   nrexcl
>> SDS   3
>> 
>> [ atoms ]
>> ; nr typeresnr   residu  atomcgnrcharge  mass
>>   1 SL  1  SDS  S  1  0.00032.0600   ; 
>> qtot  1.330
>>   2OSL  1  SDSOS1  2  0.00015.9994   ; 
>> qtot  1.050
>>   3O2L  1  SDSOS2  3  0.00015.9994   ; 
>> qtot  0.400
>>   4O2L  1  SDSOS3  4  0.00015.9994   ; 
>> qtot -0.250
>>   5O2L  1  SDSOS4  5  0.00015.9994   ; 
>> qtot -0.900
>>.
>>.
>>  25   HAL2  1  SDSH71 25  0.000 1.0080   ; 
>> qtot -1.090
>>  26   HAL2  1  SDSH72 26  0.000 1.0080   ; 
>> qtot -1.000
>>  27   CTL2  1  SDS C8 27  0.00012.0110   ; 
>> qtot -1.180
>>   .
>>   .
>>  42   HAL3  1  SDS   H123 42  0.000 1.0080   ; 
>> qtot -1.000
>>  43SOD  2  SDSSOD 43  0.00022.9898   ; 
>> qtot  1.000
>> .
>> 
>> However I get this warning during the simulation :
>> 
>> WARNING: Listed nonbonded interaction between particles 25 and 43
>> at distance 2.303 which is larger than the table limit 2.200 nm.
>> 
>> Do you have any idea how could I get rid off this warning?
>> 
> 
> This is a generic simulation failure message, indicating that your system 
> is blowing up.  This could be due to any number of reasons, but without 
> more details it's pointless to guess.
> 
>> Also does the hacked .top file seem correct?
>> 
> 
> Decoupling the Na+ ion will mean your 

Re: [gmx-users] Protein simulation, improve GPU/CPU ratio

[Justin Lemkul]

On 11/3/16 1:48 PM, Matilde Viegas wrote:

Dear all,

I have a few questions regarding a simulation system containing a protein
in a box of water, with ions. Just like the lysozyme tutorial:

my system is a 5000 residue enzyme (75600 atoms), in a triclinic TIP3P
water box of a total 1567103 atoms (around 50 water molecules). My
input is:

; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to
perform
define = -DFLEXIBLE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 40; Frequency to update the neighbor list
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
coulombtype = Reaction-Field; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
(yes/no)

Unfortunately, my GPU/CPU ratio is 16= Force evaluation time GPU/CPU:
345.675 ms/20.818 ms = 16.605

Any ideia on how I can improve the ratio?



Energy minimization is a poor way to evaluate performance of your hardware.  Do 
a real MD run and inspect the .log file.  The end has a detailed performance 
breakdown of exactly how mdrun spent all its time.


-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.

Re: [gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

On 11/3/16 10:56 AM, gozde ergin wrote:

You can decouple atomic and molecular ions, there are just additional 
considerations like an interface potential to calculate.  See, e.g. work by 
Benoit Roux.


Yes I can but do I need to? I just want to know the free energy of solvation of 
SDS. If I do not include the Na ion decoupling, is it wrong?



If you want the hydration free energy of SDS, you should not include Na+ because 
the simultaneous decoupling will include the hydration free energy of Na+.  You 
can subtract that out, but there is error associated with that calculation and 
accounting for that is not necessarily easy.  It is straightforward to just deal 
with SDS alone.


-Justin


On 02 Nov 2016, at 12:42, Justin Lemkul  wrote:



On 11/1/16 9:02 AM, gozde ergin wrote:

This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


If I do not include the Na ion in decoupling I do not have this warning.
If I do not decouple Na ion still I need to make the charge of this molecule 
zero otherwise system charge becomes +1.


Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.


My purpose is doing the same thing with SDS that you did with Methane. And as 
SDS has Na ion I thought I need also to decouple it.
Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
Last question even if I do not decouple the Na ion I need to make it charge 
zero, right?



You can decouple atomic and molecular ions, there are just additional 
considerations like an interface potential to calculate.  See, e.g. work by 
Benoit Roux.

-Justin


Thanks in advance.

On 01 Nov 2016, at 13:21, Justin Lemkul  wrote:



On 11/1/16 7:31 AM, gozde ergin wrote:

Hi Justin,

I would like to ask one question related to this tutorial. I do the same thing 
with using SDS (Sodium dodecyl sulfate) molecule.
As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate part. 
However in order to estimate the free energy of SDS salvation in water I need 
to decouple the all SDS molecule. Since couple-moltype accept only one types of 
molecule, I hacked the topology and put all atoms I want to decouple in the 
same [moleculetype] :

[ moleculetype ]
; name  nrexcl
SDS  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
   1 SL  1  SDS  S  1  0.00032.0600   ; qtot  
1.330
   2OSL  1  SDSOS1  2  0.00015.9994   ; qtot  
1.050
   3O2L  1  SDSOS2  3  0.00015.9994   ; qtot  
0.400
   4O2L  1  SDSOS3  4  0.00015.9994   ; qtot 
-0.250
   5O2L  1  SDSOS4  5  0.00015.9994   ; qtot 
-0.900
.
.
  25   HAL2  1  SDSH71 25  0.000 1.0080   ; qtot 
-1.090
  26   HAL2  1  SDSH72 26  0.000 1.0080   ; qtot 
-1.000
  27   CTL2  1  SDS C8 27  0.00012.0110   ; qtot 
-1.180
   .
   .
  42   HAL3  1  SDS   H123 42  0.000 1.0080   ; qtot 
-1.000
  43SOD  2  SDSSOD 43  0.00022.9898   ; qtot  
1.000
.

However I get this warning during the simulation :

WARNING: Listed nonbonded interaction between particles 25 and 43
at distance 2.303 which is larger than the table limit 2.200 nm.

Do you have any idea how could I get rid off this warning?



This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


Also does the hacked .top file seem correct?



Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.

-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 

Re: [gmx-users] Energy Minimization

[Justin Lemkul]

On 11/3/16 10:11 AM, Mishelle Oña wrote:

Positive values of potential energy and I am in vacuo.


Your outcome is exactly what you should expect.  Energies can be positive, and 
almost always are when doing work in vacuo.  The net negative energy in 
condensed phase is driven by attractive solute-solvent and solvent-solvent 
interactions, of which you have none in the gas phase.


-Justin


Mishelle



Sent from my Samsung device


 Original message 
From: Justin Lemkul 
Date: 11/03/2016 08:43 (GMT-05:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Energy Minimization



On 11/2/16 9:40 PM, Mishelle Oña wrote:

Hello

I have a question about energy minimization tool. I am modelling a polymer and 
I use a force field I have developed. I have run a EM and got positive values. 
Can you help me with this?



Positive values for what?  Are you in vacuo or in solvent?

-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] Simulation of a solid surface within Gromacs (Justin Lemkul)

[Justin Lemkul]

On 11/3/16 9:51 AM, Kamps, M. wrote:

Dear Justin, GMX-users,

First of all, thank you for the reply.
I'm not really sure how to continue from this, there is no entry in the
manual for either the command x2top or .n2t files. Google does provide some
information but only limited.
According to the information on x2top the supported input files are:

 -f  [<.gro/.g96/...>]  (conf.gro)
   Structure file: gro g96 pdb brk ent esp tpr

Where should I use this n2t file, since it is not listed? I've found this
small tutorial:

http://chembytes.wikidot.com/grocnt , with this example n2t file:

; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes
; Andrea Minoia
HHJ0.00   1.008  1C 0.109
;Hydrogen
CCJ0.00  12.011  3C 0.142   H 0.109   H 0.109
;Periferic C
CCJ0.00  12.011  3C 0.142   C 0.142   H 0.108
;Periferic C
CCJ0.00  12.011  1C 0.142
;Internal/periodic C
CCJ0.00  12.011  2C 0.142   C 0.142
;Internal/periodic C
CCJ0.00  12.011  3C 0.142   C 0.142   C 0.142
;Internal/periodic C

According to this file, the n2t file consists only of the molecules, its
name, its charge, weight, number of connections, and connected atoms? Is
this correct?



Yep, basically.  I had written a page on the .n2t file for the wiki, but it got 
nuked in the documentation overhaul and apparently there is no longer official 
documentation for the .n2t file.  I'll try to see if we can get that fixed.



I'm kind of stuck as to how to proceed. I'm trying to implement a surface
into gromacs. This surface is obviously inorganic and can either be
metallic or ceramic, bonded or non-bonded. Is this possible?


If it's all held together with nonbonded interactions, then you really don't 
need to do much of anything.  Define the atom types and their parameters, and 
off you go.  The topology can be written by pdb2gmx using single-atom .rtp 
entries for the different atoms.  A bit of a hack, but should work just fine. 
Something that requires bonds and an infinite representation can only be built 
with x2top.


-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] PhD position at MEMPHYS: Centre for Biomembrane Physics, Denmark

[himanshu khandelia]

Dear All,

A PhD scholarship in computer simulations of ion transport in biology is
available at the Department of Physics, Chemistry and Pharmacy (FKF) at the
University of Southern Denmark (www.sdu.dk) starting as soon as possible.
The position is associated with the MEMPHYS-Center for Biomembrane Physics.
Outstanding candidates comfortable in the Linux computing environment, and
from backgrounds in physical chemistry, engineering, computer science,
physics and similar areas are invited to apply. Candidates should have a
strong physics/chemistry background. Knowledge of computer simulations is
desired, but can be acquired during the job. Knowledge of computer
programming is desired, preferably in C or C++.

The candidate will be working on an interdisciplinary project involving
molecular biophysics, structural biology and computer simulations. The
project involves using multi-scale simulations to investigate the
fundamental molecular basis of proton ion transport across biological
membranes through proteins. Strong collaboration with experimental groups
is expected and the successful candidate will work in a highly
collaborative atmosphere at MEMPHYS, working together with theorists and
experimental scientists. The project is co-advised by Associate Professors
Himanshu Khandelia and Ilia Solov’yov. The successful candidate will have
access to large-scale resources ABACUS 2.0:  www.deic.sdu.dk

Applications and queries can be sent to Dr. Khandelia (hkhan...@sdu.dk). In
the subject of your application, please use the keyword: PROTOPORT. Please
see https://himanshukhandelia.wordpress.com/ for more information of
activities in the group.

Please apply at: https://goo.gl/DqosIz

Application Deadline: Nov. 17, 2016



-
Himanshu Khandelia, PhD
Associate Professor
MEMPHYS, Center for BioMembrane Physics
University of Southern Denmark (SDU)
Campusvej 55, Odense M 5230, Denmark
hkhan...@sdu.dk
-
-- 
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.