[gmx-users] Performing energy minimisation for an alanine scan

2018-07-07 Thread Anthony Nash
I'm trying to minimise 600+ structure. They differ by an alanine substitution, 
which has been put in place using stateA/stateB topologies. The technique used 
to generate the initial structure was taken from: 
http://pmx.mpibpc.mpg.de/output.pl?jobid=model_scanA_amber99sb-star-ildn-mut.ff_3329_20180703151957


This produces a topology of:

stateA -> wildtype amino acid

stateB -> alanine substitution


Given the number of structures, I am trying to automate everything. Centering, 
solvating, genion etc., all done. Now I come to an initial energy minimisation 
for each structure. Unfortunately, emtol is aren't falling < 1000, which I find 
to be a value sufficient to move on from energy minimisation to more dynamical 
equilibrium methodologies. One could argue that I should look at the 
trajectory, but I want the parameters correct first, especially given how I am 
automating this.


Since the alanine scan methodology generated stateA/stateB topologies per 
structure, I figured that I need to use free energy parameters in my .mdp file 
to ensure that I am immediately only ever using the stateB (alanine) topology.


I basically need someone to sanity check the .mdp values to ensure that I only 
use stateB (the alanine topology) during the energy minimisation. The complete 
free energy .mdp values (from the mdout.mdp) file are:


; Free energy variables
free-energy  = yes
couple-moltype   =
couple-lambda0   = vdw-q
couple-lambda1   = vdw-q
couple-intramol  = no
init-lambda  = -1
init-lambda-state= 0
delta-lambda = 0
nstdhdl  = 10
fep-lambdas  =
mass-lambdas =
coul-lambdas = 1.0
vdw-lambdas  = 1.0
bonded-lambdas   = 1.0
restraint-lambdas= 1.0
temperature-lambdas  =
calc-lambda-neighbors= 1
init-lambda-weights  =
dhdl-print-energy= no
sc-alpha = 0
sc-power = 1
sc-r-power   = 6
sc-sigma = 0.3
sc-coul  = no
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1

Please note, key-value pairs like coul-lambdas and vdw-lambdas are 1.0 as I 
only want to model state B and I am not interested in slow growth.


Are these parameters sufficient for modelling stateB upon immediate execution 
of an energy minimisation (and NPT/NVT dynamics)? I've had very little 
experience with the lambda implementation in gromacs and I turn to more 
experience.


Many thanks

Anthony


Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford
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Re: [gmx-users] How to get the complete molecule?

2018-07-07 Thread Victor Rosas Garcia
try "-pbc whole" instead of "-pbc mol"

El sáb., 7 jul. 2018 a las 2:13, Anjana Jayasinghe ()
escribió:

> Dear All,
> In my simulation, part of my molecule is in a one cell and the other part
> is in the adjacent cell. I want to get the complete molecule in the pdb
> format in the center of the box. I tried to do that using gmx trjconv -f
> run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut I
> couldn't get what I want. Can anyone help me?
> Thank you.
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Re: [gmx-users] building GROMACS 2018.2

2018-07-07 Thread Benson Muite

May wish to use ccmake and check correct links to Cuda are done.

On 07/07/2018 08:11 PM, Sevahn Kayaneh Vorperian wrote:

Dear All,

I am new to GROMACS and wanted to build the 2018.2 version so that I can do 
some MD work.

I am following the instructions under "Quick and Dirty Installation" verbatim: 
http://manual.gromacs.org/documentation/2018/install-guide/index.html

I got the latest version of CUDA and CMAKE. I didn't bother with MPI support 
since I'm not running on multiple networks. For FFT, I did the following during 
the cmake step to acquire it
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

this went fine, as well as the make command

however, during make check, I got an error at 97%

(where terminal said: Linking CXX shared library 
../../../../lib/libgpu_utilstest_cuda.dylib); attaching the output I got here.

I ran the commands in the folder I made called build-gromacs not build; that 
was the only difference from the documentation in the manual, but the correct 
folders were referenced, so it shouldn’t be a problem.

I'm unsure how to proceed from here, and what adjustments I need to make so 
that I can finish building GROMACS.

Would really appreciate guidance…
I saw previous problems posted on the site where people got stuck at 2 or 3% 
during the build with similar terminal output with it crashed, but the 
resolution for how to get past this was unclear.

Thanks!
Sevahn


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Re: [gmx-users] Force field parameter

2018-07-07 Thread Soham Sarkar
I have already mailed them... waiting for their reply..

On Sat, 7 Jul 2018, 11:22 pm Mark Abraham,  wrote:

> Hi,
>
> Your other good approach is to contact the authors to ask them to share
> their methodology fully, ie force field files.
>
> Mark
>
> On Sat, Jul 7, 2018, 13:47 Soham Sarkar  wrote:
>
> > Dear All,
> >  Can anyone please tell me, where from I get the parameters
> for
> > Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is
> > already in GROMACS? I have got the files for the KBFF force field but not
> > these three.  The paper by Dias and group
> > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.108102
> used
> > different force field. I want to go that way.Please provide me with the
> > links or relevant websites for the filese regarding the force field.
> Thanks
> > in advance.
> > -Soham
> >
> > --
> > 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
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] building GROMACS 2018.2

2018-07-07 Thread Sevahn Kayaneh Vorperian
Dear All,

I am new to GROMACS and wanted to build the 2018.2 version so that I can do 
some MD work.

I am following the instructions under "Quick and Dirty Installation" verbatim: 
http://manual.gromacs.org/documentation/2018/install-guide/index.html

I got the latest version of CUDA and CMAKE. I didn't bother with MPI support 
since I'm not running on multiple networks. For FFT, I did the following during 
the cmake step to acquire it
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

this went fine, as well as the make command

however, during make check, I got an error at 97%

(where terminal said: Linking CXX shared library 
../../../../lib/libgpu_utilstest_cuda.dylib); attaching the output I got here.

I ran the commands in the folder I made called build-gromacs not build; that 
was the only difference from the documentation in the manual, but the correct 
folders were referenced, so it shouldn’t be a problem.

I'm unsure how to proceed from here, and what adjustments I need to make so 
that I can finish building GROMACS.

Would really appreciate guidance…
I saw previous problems posted on the site where people got stuck at 2 or 3% 
during the build with similar terminal output with it crashed, but the 
resolution for how to get past this was unclear.

Thanks!
Sevahn
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Re: [gmx-users] Force field parameter

2018-07-07 Thread Mark Abraham
Hi,

Your other good approach is to contact the authors to ask them to share
their methodology fully, ie force field files.

Mark

On Sat, Jul 7, 2018, 13:47 Soham Sarkar  wrote:

> Dear All,
>  Can anyone please tell me, where from I get the parameters for
> Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is
> already in GROMACS? I have got the files for the KBFF force field but not
> these three.  The paper by Dias and group
> https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.108102 used
> different force field. I want to go that way.Please provide me with the
> links or relevant websites for the filese regarding the force field. Thanks
> in advance.
> -Soham
>
> --
> 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!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Force field parameter

2018-07-07 Thread Soham Sarkar
Dear All,
 Can anyone please tell me, where from I get the parameters for
Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is
already in GROMACS? I have got the files for the KBFF force field but not
these three.  The paper by Dias and group
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.108102 used
different force field. I want to go that way.Please provide me with the
links or relevant websites for the filese regarding the force field. Thanks
in advance.
-Soham

-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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[gmx-users] How to get the complete molecule?

2018-07-07 Thread Anjana Jayasinghe
Dear All,
In my simulation, part of my molecule is in a one cell and the other part is in 
the adjacent cell. I want to get the complete molecule in the pdb format in the 
center of the box. I tried to do that using gmx trjconv -f run.pdb -s run.tpr 
-pbc mol -ur compact -center -o run_new.pdbBut I couldn't get what I want. Can 
anyone help me?
Thank you.
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