Re: [gmx-users] residue error

[Quyen V. Vu]

This is nonstandard residue so GROMACS does not have database about it.
you need to generate database consistent with your forcefield

On Mon, Feb 26, 2018 at 11:22 PM, Radhika Arora  wrote:

> Hello,
>
> I face an error Residue 'BGL' not found in residue topology database.
> Please let me know how shall i rectify this and what do i need to write in
> place of BGL.
>
>
> HETATM 1700  C   BGL 1  29.680 -48.720 -19.563  0.00 -0.02
>  .177 C
> HETATM 1701  C   BGL 1  13.970 -44.542 -17.378  0.00 -0.02
>  .177 C
> HETATM 1702  C   BGL 1   6.116 -42.453 -16.285  0.00 -0.02
>  .177 C
> HETATM 1703  C   BGL 1  -1.739 -40.364 -15.193  0.00 -0.02
>  .177 C
> HETATM 1704  C   BGL 1  -9.594 -38.274 -14.101  0.00 -0.02
>  .177 C
> HETATM 1705  C   BGL 1  21.826 -46.631 -18.470  0.00 -0.02
>  .177 C
> HETATM 1706  C   BGL 1  43.915  -4.197   5.342 -0.01 -0.05
>  .178 C
> HETATM 1707  C   BGL 1  47.803  -0.833   8.026 -0.01 -0.05
>  .178 C
> HETATM 1708  C   BGL 1  46.897   4.435  10.275 -0.00 -0.05
>  .178 C
> HETATM 1709  C   BGL 1  50.785   7.800  12.959  0.00 -0.05
>  .178 C
> HETATM 1710  C   BGL 1  49.879  13.068  15.208  0.00 -0.04
>  .178 C
> HETATM 1711  C   BGL 1  53.767  16.432  17.892  0.00 -0.04
>  .178 C
> HETATM 1712  C   BGL 1  52.861  21.700  20.141  0.00 -0.03
>  .178 C
> HETATM 1713  C   BGL 1  56.749  25.064  22.825  0.00 -0.03
>  .178 C
> HETATM 1714  C   BGL 1  55.843  30.333  25.074  0.00 -0.03
>  .178 C
> HETATM 1715  C   BGL 1  59.731  33.697  27.758  0.00 -0.03
>  .178 C
> HETATM 1716  C   BGL 1  44.820  -9.465   3.093  0.00 -0.05
>  .178 C
> HETATM 1717  C   BGL 1  40.933 -12.829   0.409  0.00 -0.05
>  .178 C
> HETATM 1718  C   BGL 1  41.838 -18.098  -1.840  0.00 -0.04
>  .178 C
> HETATM 1719  C   BGL 1  37.951 -21.462  -4.524  0.00 -0.04
>  .178 C
> HETATM 1720  C   BGL 1  38.856 -26.730  -6.773  0.00 -0.03
>  .178 C
>
> ‌
> --
> 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.

[gmx-users] Simulation for Metalloprotein

[Sankaran SV .]

Hi users,

Whether it is possible to run the simulation for protein with metal
(calcium) ?
If so, what are the force fields that can be used ?
How those force fields must be altered in order to run the simulation.


-- 
Sankaran.s.v
bbin
-- 
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] cpu/gpu utilization

[Szilárd Páll]

Hi,

Please provide details, e.g. the full log so we know what version, on what
hardware, settings etc. you're running.



--
Szilárd

On Mon, Feb 26, 2018 at 8:02 PM, Mahmood Naderan 
wrote:

> Hi,
>
> While the cut-off is set to Verlet and I run "gmx mdrun -nb gpu -deffnm
> input_md", I see that 9 threads out of total logical 16 threads are running
> on the cpu while the gpu is utilized. The gmx also says
>
>
> No option -multi
> Using 1 MPI thread
> Using 16 OpenMP threads
>
>
> I want to know, why 9 threads are running?
> Is that normal? Ryzen 1800x has 8 physical cores.
>
>
> Regards,
> Mahmood
> --
> 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.

[gmx-users] cpu/gpu utilization

[Mahmood Naderan]

Hi,

While the cut-off is set to Verlet and I run "gmx mdrun -nb gpu -deffnm 
input_md", I see that 9 threads out of total logical 16 threads are running on 
the cpu while the gpu is utilized. The gmx also says


No option -multi
Using 1 MPI thread
Using 16 OpenMP threads 


I want to know, why 9 threads are running? 
Is that normal? Ryzen 1800x has 8 physical cores. 


Regards,
Mahmood
-- 
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] Anisotropic Pressure Coupling

[Adriaan Riet]

Hello,

I've been trying to run a simulation using anisotropic pressure coupling (I
want to allow the box to adjust to the right size for a zero-pressure
simulation). I am using the following settings in the .mdp file:

Pcoupl   =  Berendsen
pcoupltype   =  anisotropic
tau_p=  2.0
compressibility  =  4.5e-05 4.5e-05 4.5e-05 0 0 0
ref_p=  0 0 0 0 0 0

I can grompp the mdp file without error, but when I try to execute mdrun on
the tpr file, I obtain the following message:

Fatal error:
Domain decomposition has not been implemented for box vectors that have
non-zero components in directions that do not use domain decomposition:
ncells
= 1 8 1, box vector[2] = -nan -nan 0.00

If I change the pressure coupling to isotropic and delete the spare matrix
components from the settings, the simulation runs without error.

Am I not properly specifying the parameters? Is there another error that I
could be missing?

Thank you,
Adriaan
-- 
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] About and index file of a monolayer...

[Joe Jordan]

This is actually pretty challenging to do, but is possible with the right
technique. Have a look at the selection commands in gmx select, which
allows the specification of x,y,z positions. If you know the mid plane of
one leaf in your bilayer, you can specify a molecule type and only take
molecules that have a center of mass within a cutoff of the leaflet mid
plane (which hopefully is on xy plane with fixed z). If you have a large
enough bilayer you may have undulations, which means that you will need to
make a more complicated selection, specifying x, y and z.

On Mon, Feb 26, 2018 at 5:58 PM, Poncho Arvayo Zatarain <
poncho_8...@hotmail.com> wrote:

>
>
> Hello gromacs users: If i have a bilayer with lipids A & B and i want to
> create an index file for the upper and lower monolayer of one lipid, for
> example: lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid
> B-UPPER. How can i do that using -n index.file?
> --
> 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.
>



-- 
Joe Jordan
-- 
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] About and index file of a monolayer...

[Poncho Arvayo Zatarain]

Hello gromacs users: If i have a bilayer with lipids A & B and i want to create 
an index file for the upper and lower monolayer of one lipid, for example: 
lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid B-UPPER. How can 
i do that using -n index.file?
-- 
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] residue error

[Justin Lemkul]

On 2/26/18 11:22 AM, Radhika Arora wrote:

Hello,

I face an error Residue 'BGL' not found in residue topology database.
Please let me know how shall i rectify this and what do i need to write in
place of BGL.


HETATM 1700  C   BGL 1  29.680 -48.720 -19.563  0.00 -0.02
  .177 C
HETATM 1701  C   BGL 1  13.970 -44.542 -17.378  0.00 -0.02
  .177 C
HETATM 1702  C   BGL 1   6.116 -42.453 -16.285  0.00 -0.02
  .177 C
HETATM 1703  C   BGL 1  -1.739 -40.364 -15.193  0.00 -0.02
  .177 C
HETATM 1704  C   BGL 1  -9.594 -38.274 -14.101  0.00 -0.02
  .177 C
HETATM 1705  C   BGL 1  21.826 -46.631 -18.470  0.00 -0.02
  .177 C
HETATM 1706  C   BGL 1  43.915  -4.197   5.342 -0.01 -0.05
  .178 C
HETATM 1707  C   BGL 1  47.803  -0.833   8.026 -0.01 -0.05
  .178 C
HETATM 1708  C   BGL 1  46.897   4.435  10.275 -0.00 -0.05
  .178 C
HETATM 1709  C   BGL 1  50.785   7.800  12.959  0.00 -0.05
  .178 C
HETATM 1710  C   BGL 1  49.879  13.068  15.208  0.00 -0.04
  .178 C
HETATM 1711  C   BGL 1  53.767  16.432  17.892  0.00 -0.04
  .178 C
HETATM 1712  C   BGL 1  52.861  21.700  20.141  0.00 -0.03
  .178 C
HETATM 1713  C   BGL 1  56.749  25.064  22.825  0.00 -0.03
  .178 C
HETATM 1714  C   BGL 1  55.843  30.333  25.074  0.00 -0.03
  .178 C
HETATM 1715  C   BGL 1  59.731  33.697  27.758  0.00 -0.03
  .178 C
HETATM 1716  C   BGL 1  44.820  -9.465   3.093  0.00 -0.05
  .178 C
HETATM 1717  C   BGL 1  40.933 -12.829   0.409  0.00 -0.05
  .178 C
HETATM 1718  C   BGL 1  41.838 -18.098  -1.840  0.00 -0.04
  .178 C
HETATM 1719  C   BGL 1  37.951 -21.462  -4.524  0.00 -0.04
  .178 C
HETATM 1720  C   BGL 1  38.856 -26.730  -6.773  0.00 -0.03
  .178 C

‌


This is the exact same problem that I replied to yesterday, just with 
BGL instead of UNL.


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-February/118832.html

Please pay attention to the free help you are given, and make an effort 
to use the resources provided to you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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] residue error

[Radhika Arora]

Hello,

I face an error Residue 'BGL' not found in residue topology database.
Please let me know how shall i rectify this and what do i need to write in
place of BGL.


HETATM 1700  C   BGL 1  29.680 -48.720 -19.563  0.00 -0.02
 .177 C
HETATM 1701  C   BGL 1  13.970 -44.542 -17.378  0.00 -0.02
 .177 C
HETATM 1702  C   BGL 1   6.116 -42.453 -16.285  0.00 -0.02
 .177 C
HETATM 1703  C   BGL 1  -1.739 -40.364 -15.193  0.00 -0.02
 .177 C
HETATM 1704  C   BGL 1  -9.594 -38.274 -14.101  0.00 -0.02
 .177 C
HETATM 1705  C   BGL 1  21.826 -46.631 -18.470  0.00 -0.02
 .177 C
HETATM 1706  C   BGL 1  43.915  -4.197   5.342 -0.01 -0.05
 .178 C
HETATM 1707  C   BGL 1  47.803  -0.833   8.026 -0.01 -0.05
 .178 C
HETATM 1708  C   BGL 1  46.897   4.435  10.275 -0.00 -0.05
 .178 C
HETATM 1709  C   BGL 1  50.785   7.800  12.959  0.00 -0.05
 .178 C
HETATM 1710  C   BGL 1  49.879  13.068  15.208  0.00 -0.04
 .178 C
HETATM 1711  C   BGL 1  53.767  16.432  17.892  0.00 -0.04
 .178 C
HETATM 1712  C   BGL 1  52.861  21.700  20.141  0.00 -0.03
 .178 C
HETATM 1713  C   BGL 1  56.749  25.064  22.825  0.00 -0.03
 .178 C
HETATM 1714  C   BGL 1  55.843  30.333  25.074  0.00 -0.03
 .178 C
HETATM 1715  C   BGL 1  59.731  33.697  27.758  0.00 -0.03
 .178 C
HETATM 1716  C   BGL 1  44.820  -9.465   3.093  0.00 -0.05
 .178 C
HETATM 1717  C   BGL 1  40.933 -12.829   0.409  0.00 -0.05
 .178 C
HETATM 1718  C   BGL 1  41.838 -18.098  -1.840  0.00 -0.04
 .178 C
HETATM 1719  C   BGL 1  37.951 -21.462  -4.524  0.00 -0.04
 .178 C
HETATM 1720  C   BGL 1  38.856 -26.730  -6.773  0.00 -0.03
 .178 C

‌
-- 
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] walls with slab of water

[Jochen Hub]

Hi,

I would use a flat-bottomed position restraint in Z-direction for this 
purpose, see the Gromacs manual.


Cheers,
Jochen

Am 25.02.18 um 10:17 schrieb Adriano Santana Sanchez:

Hi,

I am trying to run a SLAB of water with a solute and I want to put a wall
on the z axis edge.

My problem is how to define *wall_atomtype *in the topology file or in the
.itp

I am using oplsaa.ff force field with SPC/E water.

This is a section of the .mpd:

Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 1
ns_type  = grid
pbc  = xy
nwall= 2
*wall_atomtype= W1 W2*
wall_type= 10-4
wall_r_linpot= -1
wall_density = 5 5
wall_ewald_zfac  = 3
ewald_geometry   = 3dc
rlist= 1.2
---
ERROR 1 [file topol.top, line 45]:
   Specified wall atom type W1 is not defined
ERROR 2 [file topol.top, line 45]:
   Specified wall atom type W2 is not defined

  Thanks,
Adriano



--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---
--
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] Keeping cis configuration of a molecule

[Justin Lemkul]

On 2/26/18 7:28 AM, Anjana Jayasinghe wrote:

Dear All,
I want to keep the cis configuration of my molecule in MD simulation. How can I 
do that? Could you please help me?


Likely you need a dihedral restraint. Refer to the manual.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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] Keeping cis configuration of a molecule

[Anjana Jayasinghe]

Dear All,
I want to keep the cis configuration of my molecule in MD simulation. How can I 
do that? Could you please help me?
Thank you.
-- 
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] g_sans calculation

[Joe Jordan]

The gmx sans and saxs tools are both using the Debeye formula to calculate
scattering angles. In gmx sans it is possible to use a monte carlo method
to limit the computational complexity of Debeye, which is O(n^2).

On Fri, Feb 23, 2018 at 9:48 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> I understand your pain, and the same could be said about gmx saxs as well.
> As Micholas said, CRYSON might be a good choice as far as implicit solvent
> methods go. Please notice that CRYSON is closed source, but it is well
> documented in the literature (it is basically a reimplementation of
> CRYSOL*).
>
> *Svergun, D., Barberato, C., & Koch, M. H. (1995). J. Appl. Crystallogr.,
> 28(6), 768-773
>
> J
>
>
> On Fri, Feb 23, 2018 at 9:14 PM, Udaya Dahal 
> wrote:
>
> >  Dear Gromacs Users,
> >
> > I am calculating the g_sans in the simulation but I am not able to find
> how
> > it is calculated. The help content is minimal. I am just wondering if
> > anyone has looked into how it is calculated (any reference to
> algorithm?).
> >
> > Regards,
> > --
> > 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.
>



-- 
Joe Jordan
-- 
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] Positive potential energy

[Mahsa]

Hi,

Thanks for your help, Justin!

Regards,
Mahsa

On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul  wrote:

>
>
> On 2/25/18 10:15 AM, Mahsa wrote:
>
>> Dear Justin,
>>
>> Thank you for your reply!
>>
>> In general, is it a good approach to first use steep algorithm for EM and
>> then to further minimize do EM with cg algorithm, on the output structure?
>>
>
> I usually don't find multiple steps of EM needed in most cases, but
> occasionally. The purpose of EM is to find a plausible starting point for
> the simulation - you can never know if you're in the global minimum so it's
> a bit of working in the dark, anyway. But the gradient (max force) reports
> on that.
>
> Could you please comment on my question about the mdp files and pbc as
>> well? Actually, you mentioned here:
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2017-February/111219.html
>>
>> that for one chain of polymer in vacuum, pbc should not be considered. So,
>> for my simulation, in the first step I have one chain in vaccum and
>> eventually I want to pack the whole box with polymer chains and ions,
>> should I use pbc or not and which of the mdp files in my first post is
>> correct?
>>
>
> If you're working in the condensed phase, you need finite cutoffs, PME,
> and PBC.
>
> -Justin
>
>
> Regards,
>> Mahsa
>>
>> On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul  wrote:
>>
>>
>>> On 2/25/18 9:26 AM, Mahsa wrote:
>>>
>>> Dear Mark,

 Thank you for your reply. However, this is not clear for me yet since I
 read this in the tutorial from Justin:

 "There are two very important factors to evaluate and determine if EM
 was
 successful. The first is the potential energy (printed at the end of the
 EM
 process, even without -v). Epot should be negative. The second important
 feature is the maximum force, Fmax, the target for which was set in
 minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater
 than
 1000 kJ mol-1 nm-1."

 So I don't know whether it is correct to continue a simulation which
 gives
 positive potential energy after the energy minimisation or not?

 And also as I mentioned in my first post (the two different mdp files),
 I
 don't know if I should consider pbc or not, in my simulation.

 Unfortunately, I didn't understand your answer to my previous questions.
 Do
 you mean that the steep integrator is not good to do energy minimization
 for this type of simulation?

 Would you please help me to fix these problems?

 There is no problem. You're just comparing apples and oranges.
>>>
>>> The tutorial system is a simple protein solvated by lots of water. The
>>> potential energy function is the sum of bonded and nonbonded terms. In an
>>> aqueous protein system, the nonbonded terms (particularly water-water
>>> electrostatics) dominate the potential energy via favorable hydrogen bond
>>> interactions. The internal (bonded) parameters for all the other species
>>> are small in magnitude, by comparison, so the nonbonded terms dominate
>>> and
>>> you get a negative potential energy.
>>>
>>> In your case, you have comparatively weak nonbonded terms and larger
>>> bonded terms, such that the potential energy function is dominated by
>>> internal energy, which is by definition, positive.
>>>
>>> This is not an indication that anything is wrong with the algorithms
>>> used.
>>>
>>> -Justin
>>>
>>>
>>> Regards,
>>>
 Mahsa

 On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham 
 wrote:

 Hi,

> Even if there are minima on the surface that have negative energy
> (which
> will depend how the model was developed, which you should look into)
> there's no reason to expect an arbitrary starting configuration will
> find
> one after a steepest descent search. A tangled pile of strings will
> stay
> tangled.
>
> Mark
>
> On Fri, Feb 23, 2018, 23:28 Mahsa E  wrote:
>
> Hello,
>
>> I want to simulate a box of polymer (32 chains) with salt. I started
>> with
>> one chain of the polymer in the box. However, after the energy
>> minimisation, the energy is still positive. I found the discussion in
>> the
>> link below very similar to the problem I have:
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2017-February/111219.html
>>
>> and tried the tips from Justin in the link but I still get positive
>>
>> energy.
>
> This is my first MDP file:
>>
>> define   =
>> integrator   = steep
>> nsteps   = -1
>> nstcgsteep   = 10
>> constraints  = none
>> lincs_order  = 8
>> emtol= 20
>> emstep   = 0.01
>>