[gmx-users] Quantification of overcharging

[Soham Sarkar]

 Dear All,
   I have a system of two ssDNA of same base sequence. I
started from lower salt concentration to the higher salt concentration,
which immediately shows charge reversal at higher charge concentration. I
want to quantify this overcharging basis on the salt concentration. Please
help me with the detail procedure, how I can show that there is
overcharging at the higher concentration regime but not at the lower
concentration. Thanks in advance.


-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
-- 
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] Gromacs installation with GPU support in Windows 7

[Jia Hong]

Aim: Install Gromacs with GPU support in windows 7


Problem: Build step failed in Visual Studio 14 2015, using CMake 3.11 GUI in 
Windows


Identified "issues":

  1.  First off, NVIDIA named their default CUDA installation directory in a 
space separated directory. This caused much grief when CMake complains that 
"Check for working NVCC/C compiler combination - broken" and "CUDA compiler 
does not seem to be functional".
 *   The solution was to surround the path with quotes in 
CUDA_TOOLKIT_ROOT_DIR
  2.  Visual Studio fails to compile libgromacs (VS complains that it could not 
find ../../lib/gromacs.lib


With regards to (2.), CMake completed the generation of VS build files without 
errors and I tried building it using VS 14 2015 (as specified in my CMake 
generation tool). The steps I took:

  1.  set the build type to Release
  2.  click build all


I also tried compiling Gromacs with the exact same steps, but without GPU 
support, and it went without a hitch.


I therefore suspect that it might be that "path issue" I faced earlier (1.), so 
I tried identifying the first error in VS build and it lead me to 
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.


I copied the commands as-is within the makefile and tried to compile it in VS 
developer command prompt myself.


The error I got was:

C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
 error: expression must be a modifiable lvalue.



My suspicion is that:

  1.  The error "might" be because of a path problem ? (like before)
  2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)


Any help would be greatly appreciated.


Regards,

Harry.

-- 
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 error

[Justin Lemkul]

On 5/21/18 5:42 PM, rose rahmani wrote:

!!!
I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get
converged.

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time so i choose 2fs...

Could you please help me which one caused to problem?


It could be any number of things, perhaps even things not listed here. 
Be a scientist - change one thing at a time until you uncover the source 
of the problem. As it stands, your system has far too many variables to 
assign blame to any one of them.


-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.thelemkullab.com

==

--
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 error

[rose rahmani]

!!!
I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get
converged.

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time so i choose 2fs...

Could you please help me which one caused to problem?

Regards
-Rose

On Tue, 22 May 2018, 01:19 Justin Lemkul,  wrote:

>
>
> On 5/21/18 4:47 PM, rose rahmani wrote:
> > Hi,
> >
> > I do umbrella sampling with GROMACS4.5.4 version. I got this error
> > "A charge group moved too far between two domain decomposition steps."
> > But when i try it in another computer(version 4.5.4 was also installed
> > there) this error doesn't exist any more! How could it be possible?which
> > one is correct?
>
> Welcome to the stochastic nature of MD. You have an unstable system that
> occasionally works. Don't trust it - figure out where the instability
> comes from and/or prepare the system more gently.
>
> -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.thelemkullab.com
>
> ==
>
> --
> 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] mdrun error

[Justin Lemkul]

On 5/21/18 4:47 PM, rose rahmani wrote:

Hi,

I do umbrella sampling with GROMACS4.5.4 version. I got this error
"A charge group moved too far between two domain decomposition steps."
But when i try it in another computer(version 4.5.4 was also installed
there) this error doesn't exist any more! How could it be possible?which
one is correct?


Welcome to the stochastic nature of MD. You have an unstable system that 
occasionally works. Don't trust it - figure out where the instability 
comes from and/or prepare the system more gently.


-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.thelemkullab.com

==

--
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 error

[rose rahmani]

Hi,

I do umbrella sampling with GROMACS4.5.4 version. I got this error
"A charge group moved too far between two domain decomposition steps."
But when i try it in another computer(version 4.5.4 was also installed
there) this error doesn't exist any more! How could it be possible?which
one is correct?

Best
-- 
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] How to put constraint

[Justin Lemkul]

On 5/21/18 4:27 PM, Tom wrote:

Dear GMX experts:


I want to constraint atoms inside a polymer.

The atoms are fixed to their relative positions,

but the whole polymer can move as a rigid body.


Can we use LINCS?


GROMACS is not well suited to rigid-body dynamics, and formally it's not 
even supported. One could assign a series of constraints, but that's 
generally unstable. I'd suggest looking into different simulation 
packages that natively support rigid-body dynamics.


-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.thelemkullab.com

==

--
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] calculating energy between certain groups

[Justin Lemkul]

On 5/21/18 10:51 AM, Irem Altan wrote:

Thanks. My .mdp file does not contain energy groups, so that was the problem. 
Given your comments about enemat giving qualitative results, is it possible to 
get interaction energy between certain groups with gmx energy? I would like to 
calculate the energy between two protein chains, between solvent and protein, 
etc. What is the correct way of doing this?


Exactly as I said, with gmx energy.

-Justin


Best,
Irem

On May 21, 2018, at 8:13 AM, Justin Lemkul 
> wrote:



On 5/20/18 9:49 PM, Irem Altan wrote:
I tried the following:

mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0

and also I can verify from the output file that it didn’t use GPUs. However, I 
still get the same error with gmx enemat:

GROMACS:  gmx enemat, version 2016.3
Executable:   /opt/gromacs/bin/gmx_mpi
Data prefix:  /opt/gromacs
Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
Command line:
   gmx_mpi enemat -f umbrella0.edr

Opened umbrella0.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 2000 time 2.000
Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
Segmentation fault

What could be the problem?

A seg fault almost always indicates buggy behavior, but you need to make sure 
you specified appropriate energygrps in the .mdp file that created the .tpr and 
that they are present in the .edr file. Note that you should probably just be 
using gmx energy to get the time series and statistics. enemat produces a 
graphical representation (qualitative) whereas energy gives a quantitative 
description.

-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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thelemkullab.com=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg=WQbAcZl9zG7WZqWA0VeI3oTiv5NXK7avLQISb6C8FN0=

==

--
Gromacs Users mailing list

* Please search the archive at 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg=xHvNWS5tpCB8uGPFxraXl6mfMeN99tD1f9pA194XNnQ=
 before posting!

* Can't post? Read 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg=bIUt7jjjzxOMl9dxnPaNNpU12qTWmyudq97uGWbcs_Y=

* For (un)subscribe requests visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg=knQRWH77KL0dXN4B_dItSwuDCqfP_cypubYLaf8ApKg=
 or send a mail to gmx-users-requ...@gromacs.org.



--
==

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.thelemkullab.com

==

--
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] calculating energy between certain groups

[Justin Lemkul]

On 5/20/18 9:49 PM, Irem Altan wrote:

I tried the following:

mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0

and also I can verify from the output file that it didn’t use GPUs. However, I 
still get the same error with gmx enemat:

GROMACS:  gmx enemat, version 2016.3
Executable:   /opt/gromacs/bin/gmx_mpi
Data prefix:  /opt/gromacs
Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
Command line:
   gmx_mpi enemat -f umbrella0.edr

Opened umbrella0.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 2000 time 2.000
Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
Segmentation fault

What could be the problem?


A seg fault almost always indicates buggy behavior, but you need to make 
sure you specified appropriate energygrps in the .mdp file that created 
the .tpr and that they are present in the .edr file. Note that you 
should probably just be using gmx energy to get the time series and 
statistics. enemat produces a graphical representation (qualitative) 
whereas energy gives a quantitative description.


-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.thelemkullab.com

==

--
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.