[gmx-users] how to set temperature-lambdas

[Qasim Pars]

Dear users,

I am confused about setting "temperature-lambdas" for free energy
calculations. I use a total of 15 lambda windows. In the mdp file, the
temperature should be 450 K at lambda = 0.5 and it symmetrically should go
to 300 K at both end states lambda=0 and lambda=1.
For this aim how should I set "temperature-lambdas" in the mdp file?

simulated-tempering = yes
sim-temp-low = 300
sim-temp-high = 450
simulated-tempering-scaling = linear
temperature-lambdas=???

Any help will be appreciated.


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[gmx-users] REMD

[Eric Smoll]

Hello GROMACS users,

As far as I understand, increasing the number of random exchanges to a
large number (mdrun suggests N^3 where N is the number of replicas) moves a
REMD simulation from a neighbor exchange procedure to a Gibbs exchange
procedure.  Can anyone provide some practical advice or references useful
in deciding which to use?  Naively, I would guess that a Gibbs exchange
procedure would converge faster for a REMD equilibration with a large
number of replicas (~100). Is this usually true?

Best,
Eric
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[gmx-users] Gromacs do oscillatory shear/box deformation?

[Smith, Micholas D.]

Greetings gromacs community


I've be thinking at looking at some viscoelastic properties and was hoping to 
avoid the slow convergence of the green-kubo method and use NEMD methods; 
however, from the manual I can't tell if the deformation options in for the mdp 
file are oscillatory or constant. So put simply: Does gromacs support 
oscillatory shear/deformations or do I need to use something else?


Thanks,


-Micholas



===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
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Re: [gmx-users] Unable to make install Gromacs on Cygwin

[Shrinath Kumar]

On 8 June 2018 at 19:35, Matthew Fisher 
wrote:

> Hi there,
>
>
> I'm wondering if anyone could help me. I've been compiling GROMACS in
> Windows using CYGWIN and this tutorial - http://megaddl.pcriot.com/
> installing-gromacs-5-1-1-in-windows-using-cygwin/
>
> However, when I go to make install, I get the following output:
>
>
> $ make install
> [  0%] Built target fftwBuild
> [  0%] Built target tng_io_zlib
> [  1%] Built target tng_io_obj
> [ 98%] Built target libgromacs
> [100%] Built target template
> [100%] Built target view_objlib
> [100%] Built target mdrun_objlib
> [100%] Built target gmx
> [100%] Built target mdrun_test_objlib
> Install the project...
> -- Install configuration: "Release"
> -- Up-to-date: /usr/local/gromacs/share/gromacs/COPYING
> CMake Error at cmake_install.cmake:31 (file):
>   file INSTALL cannot set permissions on
>   "/usr/local/gromacs/share/gromacs/COPYING"
>
>
> Any idea what I should do to rectify this?
>
>
> Thanks,
>
> Matthew
>
>
> Matthew Fisher
> DPhil Candidate in Inorganic Chemistry (L.L.Wong Group)
> Junior Dean, St Catherine’s College
>


 usr/local is typically owned by root so you can do "sudo make install" or
change the install prefix to somewhere you have permission like /home/user/
gromacs
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[gmx-users] Unable to make install Gromacs on Cygwin

[Matthew Fisher]

Hi there,


I'm wondering if anyone could help me. I've been compiling GROMACS in Windows 
using CYGWIN and this tutorial - 
http://megaddl.pcriot.com/installing-gromacs-5-1-1-in-windows-using-cygwin/

However, when I go to make install, I get the following output:


$ make install
[  0%] Built target fftwBuild
[  0%] Built target tng_io_zlib
[  1%] Built target tng_io_obj
[ 98%] Built target libgromacs
[100%] Built target template
[100%] Built target view_objlib
[100%] Built target mdrun_objlib
[100%] Built target gmx
[100%] Built target mdrun_test_objlib
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /usr/local/gromacs/share/gromacs/COPYING
CMake Error at cmake_install.cmake:31 (file):
  file INSTALL cannot set permissions on
  "/usr/local/gromacs/share/gromacs/COPYING"


Any idea what I should do to rectify this?


Thanks,

Matthew


Matthew Fisher
DPhil Candidate in Inorganic Chemistry (L.L.Wong Group)
Junior Dean, St Catherine’s College


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[gmx-users] Problem with freeze groups

[Ondrej Kroutil]

Hi gromacs users again,
I have a problem with freezing of the atoms in my simulations.
I have prepared kaolinite surface and have tried to run NVT simulation (see
attached mdp file) with frozen outer layers (BULK section in my index
file). I run it with GPU.
While in 2016.5 version everything works properly, in 2018.1 I see that in
outer layers bond distances and angles are completely frozen but slabs as a
whole move. See multiple .gro file in link:

https://drive.google.com/file/d/0Byl8CD_rdzQOenVXUGlkWFZKMHlkR1BmVjB3bnYwcERZNEVR/view?usp=sharing
https://drive.google.com/file/d/0Byl8CD_rdzQOLVc5RTZTeUg1dkpjQUJlaFZpbXM4eFFTdENj/view?usp=sharing

Please, what do you think about it? Is it a bug or my bad compilation or
bad input setting?

Thank a lot and have a nice day.

Ondřej Kroutil

https://scholar.google.cz/citations?user=vFX-JpoJ=cs

P.S. Here is the beginning of my log file...

Command line:
  gmx mdrun -nt 6 -deffnm nvt-prod

GROMACS version:2018.1
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:CUDA
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2018-05-10 11:29:37
Built by:   mrdizzy@otto [CMAKE]
Build OS/arch:  Linux 3.16.0-4-amd64 x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Build CPU family:   6   Model: 94   Stepping: 3
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.9.2
C compiler flags:-march=core-avx2 -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 4.9.2
C++ compiler flags:  -march=core-avx2-std=c++11   -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler:  /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=
compute_30,code=sm_30;-gencode;arch=compute_35,code=
sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=
compute_50,code=sm_50;-gencode;arch=compute_52,code=
sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;;
;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-
loops;-fexcess-precision=fast;
CUDA driver:8.0
CUDA runtime:   7.50


Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Family: 6   Model: 94   Stepping: 3
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel
lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Basic
Sockets, cores, and logical processors:
  Socket  0: [   0   4] [   1   5] [   2   6] [   3   7]
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 1070, compute cap.: 6.1, ECC:  no, stat:
compatible


-- 
Ondřej Kroutil
,,  Faculty of Science
   "))' University of South Bohemia
 OOO   Branisovska 1760, Ceske Budejovice, 370 05
  OOO  The Czech Republic
| OO E-mail:  okrou...@gmail.com
>--O Mobile:  +420 736 537 190
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[gmx-users] Handling PBC for Free energy calculations in plumed patched Gromacs

[Abhinandan Panigrahi]

Dear all,

I am trying to study free energy profiles for base flipping in a
DNA+Protein system via
umbrella sampling calculations on Gromacs 2016.3 patched with PLUMED 2.4.1.

On visualizing the GRO file which comes after equilibriation (and which is
used to make
the initial TPR that each window uses), I saw that part of the DNA molecule
has moved out
of the PBC box. The atoms in the DNA concerning my collective variable are
also coming out
of the PBC box (my system is huge, and the water box is not too big).

Simulations run using TPR generated from this GRO file have resulted in
profiles that are
most likely, incorrect (scatter data from production runs is far from the
minima obtained
in the PMF).

Q1) To make sure that the PLUMED calculations start with the entire system
inside the PBC
box, should I apply the trjconv command to the equilibriation GRO file, and
use `-pbc mol`
and `-pbc nojump` in succession to bring the part of the DNA that went
outside the box
back inside it. This file will then be used to generate the initial tpr.

Q2) In the PLUMED config file where I apply my restraints, I use the command
`WHOLEMOLECULE ENTITY0:`, which as per my
understanding,
handles PBC for PLUMED calculations of the CVs. Does this conflict with the
PBC treatment
that GROMACS uses?

My CVs are angular in nature (bias applied over 2 dihedrals). The protocol
for umbrella
sampling was as follows:

- equilibriate system well (total 5ns of nvt + npt runs)
- use the gro file generated above to make initial tpr, which is used by
each umbrella
sampling window
- restraints/bias is defined in plumed data files passed to mdrun with
-plumed flag
- run wham on plumed generated colvars to build pmf

Thanks in advance,

-- 
Abhinandan Panigrahi

"To make an apple pie from scratch, you must invent the universe."
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Re: [gmx-users] Regarding rigidity of water models

[João Henriques]

Hi,

[1] CHARMM36 is to be used with the CHARMM-modified TIP3P water model
(TIP3P with LJ parameters on the water molecule hydrogen atoms).

[2] By default it's rigid, but check "define =" under your mdout.mdp file.
If there's no -DFLEXIBLE, then it's rigid.

[3] No idea of what that is, sorry.

Cheers,
J
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[gmx-users] Regarding rigidity of water models

[Dilip.H.N]

Hello all,
I have done a simulation with amino-aid+cosolvent+water in which for the
amino-acid and co-solvent i have used charmm36 FF and SPC model for water.

I have a few Doubts:-

1) Is this SPC water model which i have used is suitable in case of
charmm36ff..?? Referring to  Justin's answer in RG--
https://www.researchgate.net/post/What_is_differences_between_tip3p_and_tips3p_water_model

2) From the literature, it states that the SPC, SPC/E, TIP3P etc are rigid
models. If then is there any stretching or bending of the bonds
happening..?? (ideally, it should not...).

3) I want to calculate the power spectrum of the water (which can give more
insights...). How can i do it in GROMACS..??

Any suggestions are highly appreciated.

Thank you.
---
With Best Regards,

Dilip.H.N
PhD Student.
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Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Dear Justin .
I have  two query

1-What can be the optimized value of rate can be taken
for pulling of  dsDNA/dsRNA using gromacs format where solvent is  aqua.
>From your umbrella sampling manual,  rate is very high like (0.01 nm/ps),
which is equal to 0.0001Angstrom/fs.

2- In pulling mdp file no random seed is discussed. But if we want to
obtain 2 or 3 different trajectory during
 pulling ( of the same system ) for  different seed, then how to give
different seed in pulling  mdp file.

Note -  In my thinking in gromacs, gen_seed  = -1 is default value.  And it
comes , when NVT is applied ( where
 velocity generation is allowed, to achieve required
temperature through maxwell distribution ). But in case of pulling, where
no velocity
 generation is allowed . Then how to calculate different
pulling simulation of the same system for different seeds.



On Tue, May 15, 2018 at 9:13 PM, Justin Lemkul  wrote:

>
>
> On 5/15/18 2:46 AM, Rakesh Mishra wrote:
>
>> Dear Justin,
>>
>> In all the respect that you have suggested is absolutely correct.
>> But I have  a question that just like a constant rate pulling
>> like - [pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm
>> per 1 ns  ( which was from your umbrella sampling)]
>>
>> Is there any formate in  gromacs  for the pulling for force rate like.
>>   0.01 pn per ps/fs  (rather than constant force  pulling)
>>
>
> I know of no such formula.
>
> -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
>
> ==
>
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>



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
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