[gmx-users] Fw: EQUILIBRATION

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi Would you please help me how can i solve my problem ? I wanna 
to do equilibrate my complex ( 4ly1 + ligand) but when use the nvt.mdp file in 
protein -ligand complex (lysosym4) tuturial in gromacs , i faced to an error:   
 step 1: One or more water molecules can not be settled. Check for bad contacts 
and/or reduce the timestep if appropriateThanks alotFarial


Sent from Yahoo Mail for iPhone


Begin forwarded message:

On Wednesday, July 5, 2017, 6:31 PM, ‪farial tavakoli‬ ‪ 
 wrote:

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but 
when I wanted to performance equilibration , i got this ERROR:  
step 1: One or more water molecules can not be settled. 
 Check for bad contacts and/or reduce the timestep if appropriate
Would you please help me to fix this problem?
These are all stages which I did:
I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands 
and water molecules from it and left just chain A and HETATM ZN A . 
I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx 
-f 4LY1.pdb -o 4LY1.gro -water spc
then made a complex.gro file which include 4LY1.gro and DRG.gro which i got 
from PRODRG site. I also copy paste ; Include ligand topology
#include "DRG.itp"

in the topology file and added DRG as a ligand in [ molecules ] directive. 
Then I defined box by using this command :
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

then defined solvate by :
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

then used grommp to assemble a .tpr file by using a .mdp file and this command :
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

that was my .mdp afile :
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and added 2 CL ions since my total charge was 2.00 because of zn ion. 

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2

then for minimization, i replaced energygroups from system to protein DRG in 
em_real.mdp. that was my em_real.mdp file:

integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol 
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = protein DRG   ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p 
topol.top -o em.tprand
gmx mdrun -v -deffnm em

GROMACS replies:
Steepest Descents converged to Fmax < 1000 in 1833 steps
Potential Energy  = -5.6356275e+05
Maximum force =  9.7815100e+02 on atom 3452
Norm of force =  3.1465845e+01

Simulation ended prematurely, no performance report will be written.
Is there any problem that simulation ended prematurely?

Then 

Re: [gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

[Peter Stern]

The pdb file is in Angstroms.  Gromacs uses nanometers, thus the decrease by a 
factor of 10 -> 1nm = 10A

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Anna 
Lohning
Sent: Friday, July 07, 2017 6:07 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Displacement of coordinates by an order of magnitude by 
pdb2gmx

Hi
I've looked all through the GROMACS documentation re actions of the PDB2GMX 
command but I cant' see a reference to why it appears to change the coordinates 
of the input .pdb file (basically decreasing them by an order of magnitude). Is 
this normal? When grepping out your docked ligands this causes problems later 
when you put the ligand coordinates back in prior to creating the box, having 
to then alter those coordinates in the same manner. I am obviously missing some 
important information!  (I using Gromacs 5.0.4) Kind regards & many thanks/Anna


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[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

[Anna Lohning]

Hi
I've looked all through the GROMACS documentation re actions of the PDB2GMX 
command but I cant' see a reference to why it appears to change the coordinates 
of the input .pdb file (basically decreasing them by an order of magnitude). Is 
this normal? When grepping out your docked ligands this causes problems later 
when you put the ligand coordinates back in prior to creating the box, having 
to then alter those coordinates in the same manner. I am obviously missing some 
important information!  (I using Gromacs 5.0.4)
Kind regards & many thanks/Anna


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[gmx-users] Generating GROMACS input file from the GAMESS output file

[조영래]

Hi gmx users~

I would like to generate *.gro *itp file about one atom for MD simulation.
So I calculated Fe metal atom using GAMESS program.
--
FE.inp   FE.dat FE.log
--
How do I make  GAMESS result file (.log) into AMBER force field format
(.gro .itp).
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Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Du, Yu]

Yeah, Thanks for the clue.

> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: Friday, July 7, 2017
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Fatal error: Invalid character in digit-only string: 
> '�'
> 
> Hi,
> 
> Yes. And it looks like you've copied and pasted a "smart quote" character
> produced from some fancy editor. If that's a tutorial or user guide, please
> ask them to fix it ;-)
> 
> Mark
> 
> On Thu, 6 Jul 2017 17:25 Hermann, Johannes 
> wrote:
> 
> > Hey Yu
> >
> > Try:
> >
> > gmx mdrun -v -ntmpi 8 -gpu_id  -deffnm nvt
> >
> > So the same command you used, but _without_ the quotation marks. That is
> > what the error tells you.
> >
> > Best
> > Johannes
> > On 06.07.2017 16:52, Du, Yu wrote:
> > > Dear Gromacs Users,
> > >
> > >
> > > I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5:
> > Protein-Ligand Complex.
> > > If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.
> > >
> > >
> > > If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will
> > get the following errors.
> > >
> > >
> > > Is this a bug or the some error with the installment.
> > > I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this
> > email.
> > > The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4
> > -DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath
> > -Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON
> > -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0
> > -DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3
> > -DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3
> > -DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256
> > -DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so
> > -DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`
> > >
> > >
> > > Thanks for any information about the error, my nvt.log file and the
> > compile command parameters.
> > >
> > >
> > > Yu
> > >
> > >
> > > ===
> > > [duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “”
> > -deffnm nvt
> > >
> > >
> > > Back Off! I just backed up nvt.log to ./#nvt.log.3#
> > >
> > >
> > > Running on 1 node with total 20 cores, 40 logical cores, 4 compatible
> > GPUs
> > > Hardware detected:
> > >CPU info:
> > >  Vendor: Intel
> > >  Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> > >  SIMD instructions most likely to fit this hardware: AVX2_256
> > >  SIMD instructions selected at GROMACS compile time: AVX_256
> > >
> > >
> > >Hardware topology: Basic
> > >GPU info:
> > >  Number of GPUs detected: 4
> > >  #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >
> > >
> > > Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this
> > machine, which is better.
> > >
> > >
> > > Reading file nvt.tpr, VERSION 2016.3 (single precision)
> > > Changing nstlist from 10 to 40, rlist from 1.4 to 1.472
> > >
> > >
> > >
> > >
> > > ---
> > > Program: gmx mdrun, version 2016.3
> > > Source file: src/gromacs/utility/cstringutil.cpp (line 583)
> > >
> > >
> > > Fatal error:
> > > Invalid character in digit-only string: '�'
> > >
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > ---
> > > ===
> > > LOG FILE:
> > >
> > > GROMACS version:2016.3
> > > Precision:  single
> > > Memory model:   64 bit
> > > MPI library:thread_mpi
> > > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> > > GPU support:CUDA
> > > SIMD instructions:  AVX_256
> > > FFT library:fftw-3.3.6-pl2-sse2-avx
> > > RDTSCP usage:   enabled
> > > TNG support:enabled
> > > Hwloc support:  disabled
> > > Tracing support:disabled
> > > Built on:   Tue Jul  4 17:23:23 CST 2017
> > > Built by:   duyu@gpu-new [CMAKE]
> > > Build OS/arch:  Linux 2.6.32-431.el6.x86_64 x86_64
> > > Build CPU vendor:   Intel
> > > Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> > > Build CPU family:   6   Model: 63   Stepping: 2
> > > Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> > lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> > sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > > C compiler: /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
> > > C 

Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Mark Abraham]

Hi,

Yes. And it looks like you've copied and pasted a "smart quote" character
produced from some fancy editor. If that's a tutorial or user guide, please
ask them to fix it ;-)

Mark

On Thu, 6 Jul 2017 17:25 Hermann, Johannes 
wrote:

> Hey Yu
>
> Try:
>
> gmx mdrun -v -ntmpi 8 -gpu_id  -deffnm nvt
>
> So the same command you used, but _without_ the quotation marks. That is
> what the error tells you.
>
> Best
> Johannes
> On 06.07.2017 16:52, Du, Yu wrote:
> > Dear Gromacs Users,
> >
> >
> > I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5:
> Protein-Ligand Complex.
> > If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.
> >
> >
> > If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will
> get the following errors.
> >
> >
> > Is this a bug or the some error with the installment.
> > I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this
> email.
> > The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4
> -DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath
> -Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON
> -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0
> -DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3
> -DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3
> -DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256
> -DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so
> -DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`
> >
> >
> > Thanks for any information about the error, my nvt.log file and the
> compile command parameters.
> >
> >
> > Yu
> >
> >
> > ===
> > [duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “”
> -deffnm nvt
> >
> >
> > Back Off! I just backed up nvt.log to ./#nvt.log.3#
> >
> >
> > Running on 1 node with total 20 cores, 40 logical cores, 4 compatible
> GPUs
> > Hardware detected:
> >CPU info:
> >  Vendor: Intel
> >  Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> >  SIMD instructions most likely to fit this hardware: AVX2_256
> >  SIMD instructions selected at GROMACS compile time: AVX_256
> >
> >
> >Hardware topology: Basic
> >GPU info:
> >  Number of GPUs detected: 4
> >  #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> >  #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> >  #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> >  #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> >
> >
> > Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this
> machine, which is better.
> >
> >
> > Reading file nvt.tpr, VERSION 2016.3 (single precision)
> > Changing nstlist from 10 to 40, rlist from 1.4 to 1.472
> >
> >
> >
> >
> > ---
> > Program: gmx mdrun, version 2016.3
> > Source file: src/gromacs/utility/cstringutil.cpp (line 583)
> >
> >
> > Fatal error:
> > Invalid character in digit-only string: '�'
> >
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > ===
> > LOG FILE:
> >
> > GROMACS version:2016.3
> > Precision:  single
> > Memory model:   64 bit
> > MPI library:thread_mpi
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> > GPU support:CUDA
> > SIMD instructions:  AVX_256
> > FFT library:fftw-3.3.6-pl2-sse2-avx
> > RDTSCP usage:   enabled
> > TNG support:enabled
> > Hwloc support:  disabled
> > Tracing support:disabled
> > Built on:   Tue Jul  4 17:23:23 CST 2017
> > Built by:   duyu@gpu-new [CMAKE]
> > Build OS/arch:  Linux 2.6.32-431.el6.x86_64 x86_64
> > Build CPU vendor:   Intel
> > Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> > Build CPU family:   6   Model: 63   Stepping: 2
> > Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > C compiler: /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
> > C compiler flags:-mavx   -Wl,-rpath
> -Wl,/home/duyu/software/gcc-4.9.4/lib64  -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> > C++ compiler:   /home/duyu/software/gcc-4.9.4/bin/g++-4.9.4 GNU 4.9.4
> > C++ compiler flags:  -mavx-std=c++0x   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> > CUDA compiler:  /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
> Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, 

Re: [gmx-users] Charge Mutation (State B) for Ions

[Hermann, Johannes]

Thank you very much, Justin!

Best

Johannes


On 06.07.2017 14:43, Justin Lemkul wrote:



On 7/6/17 8:42 AM, Hermann, Johannes wrote:

Dear Justin,

I think you were referring to amitabhjayas...@gmail.com Mails, right? 
You posted the link as answer to his question but now my object is in 
the object line.




Yes, because it was important to correct the record and because 
failing to change the subject and replying to the whole digest is 
incorrect list etiquette.



However, I am still looking for an answer to my question.

Is there anyone, who can tell me something about my dual topology of 
my MG ions or point me to some literature? I really did my google 
search before...




Your approach is fine.

-Justin


I will highly appreciate it!

Thanks!

Johannes

---

This was my orginal message:

Dear all,

I am doing a FEC via alchemical transformation. In order to keep the 
charge constant I plan to mutate ions at the same time. In 
particular, I want to change the charge of MG ions. My question is 
did I manipulate the .top .itp and .gro file in the right way:


In the topology.top file I added:

#include "topol_MG_Hybrid.itp"

in the beginning and included in the [molecules] section

MG_HBRID26

at the place where my hybrid MGs begin in the .gro file. In the .tip 
file I defined the new moleculetype and the atom:


[ moleculetype ]
; Namenrexcl
MG_HBRID 1
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge mass typeB 
chargeB  massB
1   MG1MGXMGHBR  1  2 24.305 
MG   2.30769  24.305


In the gro file I changed the (formaly regular) MGs to:

8702MGX  MGHBR55183  -1.480   0.077   2.991

I.e. I changed the residue name to MGX and the atom name to MGHBR. I 
ran grompp and it compiles without errors. However, I want to make 
sure, that this is consistent with gromacs files and that I will 
change the charge in the simulation.


Thank you very much for your help!

All the best
Johannes

---

On 06.07.2017 14:24, Justin Lemkul wrote:



On 7/6/17 12:56 AM, amitabh jayaswal wrote:

... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is 
what I'm

repeatedly getting.
Please rectify/improve.


Because you haven't copied the whole URL, which is split across two 
lines in that message.


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html 



-Justin







--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Hermann, Johannes]

Hey Yu

Try:

gmx mdrun -v -ntmpi 8 -gpu_id  -deffnm nvt

So the same command you used, but _without_ the quotation marks. That is 
what the error tells you.


Best
Johannes
On 06.07.2017 16:52, Du, Yu wrote:

Dear Gromacs Users,


I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5: Protein-Ligand 
Complex.
If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.


If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will get the 
following errors.


Is this a bug or the some error with the installment.
I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this email.
The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4 
-DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath 
-Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON 
-DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0 
-DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3 
-DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3 
-DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256 
-DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so 
-DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`


Thanks for any information about the error, my nvt.log file and the compile 
command parameters.


Yu


===
[duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “” -deffnm 
nvt


Back Off! I just backed up nvt.log to ./#nvt.log.3#


Running on 1 node with total 20 cores, 40 logical cores, 4 compatible GPUs
Hardware detected:
   CPU info:
 Vendor: Intel
 Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
 SIMD instructions most likely to fit this hardware: AVX2_256
 SIMD instructions selected at GROMACS compile time: AVX_256


   Hardware topology: Basic
   GPU info:
 Number of GPUs detected: 4
 #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
 #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
 #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
 #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible


Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this 
machine, which is better.


Reading file nvt.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1.4 to 1.472




---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/utility/cstringutil.cpp (line 583)


Fatal error:
Invalid character in digit-only string: '�'


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
===
LOG FILE:

GROMACS version:2016.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:CUDA
SIMD instructions:  AVX_256
FFT library:fftw-3.3.6-pl2-sse2-avx
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   Tue Jul  4 17:23:23 CST 2017
Built by:   duyu@gpu-new [CMAKE]
Build OS/arch:  Linux 2.6.32-431.el6.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Build CPU family:   6   Model: 63   Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx 
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 
sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
C compiler flags:-mavx   -Wl,-rpath -Wl,/home/duyu/software/gcc-4.9.4/lib64 
 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler:   /home/duyu/software/gcc-4.9.4/bin/g++-4.9.4 GNU 4.9.4
C++ compiler flags:  -mavx-std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
CUDA compiler:  /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
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;-ccbin=/home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4;;;-Xcompiler;,-mavx,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
CUDA driver:7.0
CUDA runtime:   7.0
===




--
__
*Technische Universität München*
*Johannes Hermann, 

[gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Du, Yu]

Dear Gromacs Users, 


I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5: Protein-Ligand 
Complex.
If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.


If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will get the 
following errors.


Is this a bug or the some error with the installment.
I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this email. 
The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4 
-DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath 
-Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON 
-DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0 
-DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3 
-DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3 
-DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256 
-DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so 
-DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`


Thanks for any information about the error, my nvt.log file and the compile 
command parameters.


Yu


===
[duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “” -deffnm 
nvt


Back Off! I just backed up nvt.log to ./#nvt.log.3#


Running on 1 node with total 20 cores, 40 logical cores, 4 compatible GPUs
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256


  Hardware topology: Basic
  GPU info:
Number of GPUs detected: 4
#0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible


Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this 
machine, which is better.


Reading file nvt.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1.4 to 1.472




---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/utility/cstringutil.cpp (line 583)


Fatal error:
Invalid character in digit-only string: '�'


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
===
LOG FILE:

GROMACS version:2016.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:CUDA
SIMD instructions:  AVX_256
FFT library:fftw-3.3.6-pl2-sse2-avx
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   Tue Jul  4 17:23:23 CST 2017
Built by:   duyu@gpu-new [CMAKE]
Build OS/arch:  Linux 2.6.32-431.el6.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Build CPU family:   6   Model: 63   Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx 
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 
sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
C compiler flags:-mavx   -Wl,-rpath -Wl,/home/duyu/software/gcc-4.9.4/lib64 
 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:   /home/duyu/software/gcc-4.9.4/bin/g++-4.9.4 GNU 4.9.4
C++ compiler flags:  -mavx-std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
CUDA compiler:  /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
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;-ccbin=/home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4;;;-Xcompiler;,-mavx,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
 
CUDA driver:7.0
CUDA runtime:   7.0
===


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[gmx-users] ACCELERATE SIMULATION

[Aman Deep]

HELLO,

I had run simulation for my protein which has 1200 residues it took 10 days
for 10 ns on simple mdrun command. I have a graphic card with the following
configuration:


  VGA compatible controller: Advanc VGA compatible controller: Advanced
Micro Devices, Inc. [AMD/ATI] Bonaire [FirePro W5100] (prog-if 00 [VGA
controller])
Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Device 030c
Physical Slot: 4
Flags: bus master, fast devsel, latency 0, IRQ 68
Memory at e000 (64-bit, prefetchable) [size=256M]
Memory at f000 (64-bit, prefetchable) [size=8M]
I/O ports at e000 [size=256]
Memory at fbe0 (32-bit, non-prefetchable) [size=256K]
Expansion ROM at fbe4 [disabled] [size=128K]
Capabilities: 
Kernel driver in use: radeon
Kernel modules: radeon
ed Micro Devices, Inc. [AMD/ATI] Bonaire  [FirePro W5100] (prog-if 00
[VGA controller])
Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Device 030c
Physical Slot: 4
Flags: bus master, fast devsel, latency 0, IRQ 68
Memory at e000 (64-bit, prefetchable) [size=256M]
Memory at f000 (64-bit, prefetchable) [size=8M]
I/O ports at e000 [size=256]
Memory at fbe0 (32-bit, non-prefetchable) [size=256K]
Expansion ROM at fbe4 [disabled] [size=128K]
Capabilities: 
Kernel driver in use: radeon
Kernel modules: radeon

can somebody please tell me command in MDRUN or how to use GPU to
accelerate the simulation?

thank you

-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] User-defined Nonbonded Potentials and Cutoff Treatment

[Phillip Rauscher]

Hello all,

I'm trying to systematically scale down the non-bonded interaction between
two specific atom types without perturbing the interactions with the other
species (basically multiplying their pair potential by 0

Re: [gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 7/6/17 8:42 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

It would be helpful if you please explain in a bit more detail about the impact of the 
settings of table-extension. The manual says "Extension of the non-bonded potential 
lookup tables beyond the largest cut-off distance", but a better insight from you 
would be definitely more very useful.

I have a slightest idea that it is useful to save computational time. It that 
is considered true, it shouldn't affect the results, should it?

I would appreciate if you could explain how increasing table-extension can 
cause permit distorted structures.

I performed a short study of the effect on increasing table-extension from 1 nm 
to 10 nm onwards in increments of 1 nm. The inter and intra molecular energies  
increased from 1 nm to 4 nm and then were almost the same and with the 
minimization without any free energy code. Hence, I suspect that 
table-extension with 4 nm onwards takes into account all interactions while the 
free energy change goes on. I would appreciate if you could offer any comment 
on my deduction.



If you increase the table-lookup length, you tell mdrun that it is OK to find 
things like 1-4 interactions at some very long distance.  Normally when a 1-4 
goes beyond 1 nm, it is a sign of trouble.  If you make it normal, you turn a 
blind eye to possible problems.



I couldn't find any distorted structures while the study though, could you 
suggest any criteria so as to consider if any structure has evolved into a 
distorted one?

Is there any other way where I can avoid the said warning other than increasing 
table-extension and maintaining couple-intramol = no in my minimizing code with 
the free energy addendum.



No idea, sorry.  And unfortunately it appears that no one else on the mailing 
list has any idea about what's going on in your system, either.  Maybe someone 
else will chip 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

==
--
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charge Mutation (State B) for Ions

[Justin Lemkul]

On 7/6/17 8:42 AM, Hermann, Johannes wrote:

Dear Justin,

I think you were referring to amitabhjayas...@gmail.com Mails, right? You posted 
the link as answer to his question but now my object is in the object line.




Yes, because it was important to correct the record and because failing to 
change the subject and replying to the whole digest is incorrect list etiquette.



However, I am still looking for an answer to my question.

Is there anyone, who can tell me something about my dual topology of my MG ions 
or point me to some literature? I really did my google search before...




Your approach is fine.

-Justin


I will highly appreciate it!

Thanks!

Johannes

---

This was my orginal message:

Dear all,

I am doing a FEC via alchemical transformation. In order to keep the charge 
constant I plan to mutate ions at the same time. In particular, I want to change 
the charge of MG ions. My question is did I manipulate the .top .itp and .gro 
file in the right way:


In the topology.top file I added:

#include "topol_MG_Hybrid.itp"

in the beginning and included in the [molecules] section

MG_HBRID26

at the place where my hybrid MGs begin in the .gro file. In the .tip file I 
defined the new moleculetype and the atom:


[ moleculetype ]
; Namenrexcl
MG_HBRID 1
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge mass typeB chargeB  
massB
1   MG1MGXMGHBR  1  2 24.305 MG   
2.30769  24.305


In the gro file I changed the (formaly regular) MGs to:

8702MGX  MGHBR55183  -1.480   0.077   2.991

I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran grompp 
and it compiles without errors. However, I want to make sure, that this is 
consistent with gromacs files and that I will change the charge in the simulation.


Thank you very much for your help!

All the best
Johannes

---

On 06.07.2017 14:24, Justin Lemkul wrote:



On 7/6/17 12:56 AM, amitabh jayaswal wrote:

... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm
repeatedly getting.
Please rectify/improve.


Because you haven't copied the whole URL, which is split across two lines in 
that message.


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html 



-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

==
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

It would be helpful if you please explain in a bit more detail about the impact 
of the settings of table-extension. The manual says "Extension of the 
non-bonded potential lookup tables beyond the largest cut-off distance", but a 
better insight from you would be definitely more very useful.

I have a slightest idea that it is useful to save computational time. It that 
is considered true, it shouldn't affect the results, should it?

I would appreciate if you could explain how increasing table-extension can 
cause permit distorted structures. 

I performed a short study of the effect on increasing table-extension from 1 nm 
to 10 nm onwards in increments of 1 nm. The inter and intra molecular energies  
increased from 1 nm to 4 nm and then were almost the same and with the 
minimization without any free energy code. Hence, I suspect that 
table-extension with 4 nm onwards takes into account all interactions while the 
free energy change goes on. I would appreciate if you could offer any comment 
on my deduction. 

I couldn't find any distorted structures while the study though, could you 
suggest any criteria so as to consider if any structure has evolved into a 
distorted one?

Is there any other way where I can avoid the said warning other than increasing 
table-extension and maintaining couple-intramol = no in my minimizing code with 
the free energy addendum.

Thank you,

Bhagyesh

- Original Message -
From: "Varvdekar Bhagyesh Rajendra" 
To: gmx-us...@gromacs.org
Sent: Friday, June 30, 2017 2:24:09 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

Dear Justin,

It would be helpful if you please explain in a bit more detail about the impact 
of the settings of table-extension. The manual says "Extension of the 
non-bonded potential lookup tables beyond the largest cut-off distance", but a 
better insight from you would be definitely more very useful.

I have a slightest idea that it is useful to save computational time. It that 
is considered true, it shouldn't affect the results, should it?

I would appreciate if you could explain how increasing table-extension can 
cause permit distorted structures. 

Is there any other way where I can avoid the said warning other than increasing 
table-extension and maintaining couple-intramol = no in my minimizing code with 
the free energy addendum.

Thank you,

Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Thursday, June 29, 2017 6:48:25 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I am getting the same following warning even after minimizing the system 
> twice using cg integrator. This is only when the free energy stuff is 
> inserted in the energy minimization code.
> 
> " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at 
> distance 3f which is larger than the table limit 3f nm.
> 
> This is likely either a 1,4 interaction, or a listed interaction inside a 
> smaller molecule you are decoupling during a free energy calculation. Since 
> interactions at distances beyond the table cannot be computed, they are 
> skipped until they are inside the table limit again. You will only see this 
> message once, even if it occurs for several interactions.
> 
> IMPORTANT: This should not happen in a stable simulation, so there is 
> probably something wrong with your system. Only change the table-extension 
> distance in the mdp file if you are really sure that is the reason. "
> 
> 
> When the system is minimized without free energy code, it shows no warning. 
> Hence, I suppose it is due to the free energy code itself with 
> couple-intramol = no.
> 
> I found the warning disappears when couple-intramol = yes. But this is not I 
> would like to do, since intra molecular interactions need not be 
> scaled/perturbed.
> 
> It's definitely true that the "listed interaction inside a smaller molecule 
> you are decoupling during a free energy calculation".
> 
> When the table-extension is increased to 4 nm with couple-intramol = no, the 
> warning again disappears. Should I go forward with this setting and how will 
> it affect the energy minimization of my system?
> 

Increasing the table-extension means mdrun will permit distorted structures 
that 
may be totally unreasonable.  It is generally unwise to increase it, and 
especially if you're increasing it that much.

-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

Re: [gmx-users] Charge Mutation (State B) for Ions

[Hermann, Johannes]

Dear Justin,

I think you were referring to amitabhjayas...@gmail.com Mails, right? 
You posted the link as answer to his question but now my object is in 
the object line.


However, I am still looking for an answer to my question.

Is there anyone, who can tell me something about my dual topology of my 
MG ions or point me to some literature? I really did my google search 
before...


I will highly appreciate it!

Thanks!

Johannes

---

This was my orginal message:

Dear all,

I am doing a FEC via alchemical transformation. In order to keep the 
charge constant I plan to mutate ions at the same time. In particular, I 
want to change the charge of MG ions. My question is did I manipulate 
the .top .itp and .gro file in the right way:


In the topology.top file I added:

#include "topol_MG_Hybrid.itp"

in the beginning and included in the [molecules] section

MG_HBRID26

at the place where my hybrid MGs begin in the .gro file. In the .tip 
file I defined the new moleculetype and the atom:


[ moleculetype ]
; Namenrexcl
MG_HBRID 1
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge mass typeB
chargeB  massB
   1   MG1MGXMGHBR  1  2 24.305 
MG   2.30769  24.305


In the gro file I changed the (formaly regular) MGs to:

8702MGX  MGHBR55183  -1.480   0.077   2.991

I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran 
grompp and it compiles without errors. However, I want to make sure, 
that this is consistent with gromacs files and that I will change the 
charge in the simulation.


Thank you very much for your help!

All the best
Johannes

---

On 06.07.2017 14:24, Justin Lemkul wrote:



On 7/6/17 12:56 AM, amitabh jayaswal wrote:

... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what 
I'm

repeatedly getting.
Please rectify/improve.


Because you haven't copied the whole URL, which is split across two 
lines in that message.


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html 



-Justin



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

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Re: [gmx-users] Acetonitrile with CHARMM ff

[Justin Lemkul]

On 7/6/17 6:34 AM, Sonia Milena Aguilera Segura wrote:

Dear Justin,

Thank you for your reply. I went trough the CHARMM forum and I found this post 
of 2007,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, 
which basically underlines the same issues I am having. I read this post before 
posting here, and this why I came with the idea of modifying the dihedral ff 
parameters, as suggested in the forum. Apparently, it may work if I set the 
amplitude k=0 and I distort the linear angle a little (maybe 179.9) in the initial 
structure. The thing is, as I say before, I have no experience modifying force 
fields, so I wouldn't what to put and where. My guess is that I would need to go 
the ffbonded.itp file and modify and add the following lines in this way:

[ angletypes ]
;  ijk  func   theta0   ktheta  ub0 
 kub
CG331CG1N1NG1T1 5   179.90   177.401600   0. 
0.00

[ dihedraltypes ]
;  ijkl  func phi0 kphi  mult
  HGA3 CG331CG1N1  NG1T1 9 0.00 0.00 1
   
[ dihedraltypes ]

; 'improper' dihedrals
;  ijkl  func phi0 kphi
  HGA3 CG331CG1N1  NG1T1 9 0.00 0.00 1

Please let me know if this makes any sense. Is it correct to modify the 
angletype or should I only modify the initial structure?



You can modify the [angletype] parameters.  A simple energy minimization will 
correct the structure.  With respect to the dihedrals, as noted in that link, 
they simply shouldn't be there.  You can do as above with a k=0 parameter (don't 
add an improper, though harmless in this case it is incorrect to add these terms 
to methyl groups).  Or, if you want to avoid adding dummy parameters, just 
remove the dihedral lines from your .top file altogether.


-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

==
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Re: [gmx-users] simulation at different temperature

[Justin Lemkul]

On 7/6/17 1:15 AM, Alex Mathew wrote:

Dear Justin,
Thanks for the reply, Could you tell me what is the unique purpose of the
REMD and where I can learn it from basics?



A simple web search will come up with numerous review articles.

The higher temperature replicas allow for more frequent barrier crossings to 
improve conformational sampling.  With adequate sampling and exchanges, your 
ground state replica, while discontinuous in temperature space, provides a 
richer conformational ensemble than one would normally get with brute-force MD 
at a constant temperature.


-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

==
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Re: [gmx-users] Charge Mutation (State B) for Ions

[Justin Lemkul]

On 7/6/17 12:56 AM, amitabh jayaswal wrote:

... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm
repeatedly getting.
Please rectify/improve.


Because you haven't copied the whole URL, which is split across two lines in 
that message.


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html

-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

==
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[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)?

[Indu Kumari]

Hello all


How to convert multi-domain protein into single bead depending on the
number of domains i.e. if a protein contains two domain. Then how to
represent it into two beads for CG-MD.
*How to convert two domains of prtoein into two beads by Conarse-grained
Molecular Dynamics (CG-MD)?*.

With regards,
*Indu Kumari*
*Research Student,*
*Department of Environmental Science,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)?

[Indu Kumari]

Good evening all,


How to convert multi-domain protein into single bead depending on the
number of domains i.e. if a protein contains two domain. Then how to
represent it into two beads for CG-MD.
*How to convert two domains of prtoein into two beads by Conarse-grained
Molecular Dynamics (CG-MD)?*.



With regards,
*Indu Kumari*
*Research Student,*
*Department of Environmental Science,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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Re: [gmx-users] Acetonitrile with CHARMM ff

[Sonia Milena Aguilera Segura]

Dear Justin, 

Thank you for your reply. I went trough the CHARMM forum and I found this post 
of 2007,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, 
which basically underlines the same issues I am having. I read this post before 
posting here, and this why I came with the idea of modifying the dihedral ff 
parameters, as suggested in the forum. Apparently, it may work if I set the 
amplitude k=0 and I distort the linear angle a little (maybe 179.9) in the 
initial structure. The thing is, as I say before, I have no experience 
modifying force fields, so I wouldn't what to put and where. My guess is that I 
would need to go the ffbonded.itp file and modify and add the following lines 
in this way:

[ angletypes ]
;  ijk  func   theta0   ktheta  ub0 
 kub
CG331CG1N1NG1T1 5   179.90   177.401600   0. 
0.00

[ dihedraltypes ]
;  ijkl  func phi0 kphi  mult
 HGA3 CG331CG1N1  NG1T1 9 0.00 0.00 1 
  
[ dihedraltypes ]
; 'improper' dihedrals 
;  ijkl  func phi0 kphi
 HGA3 CG331CG1N1  NG1T1 9 0.00 0.00 1 

Please let me know if this makes any sense. Is it correct to modify the 
angletype or should I only modify the initial structure?

Is there someone who has already done simulations with acetonitrile? Any advice 
and feedback is very much welcome!!

Thank you very much, 

Have a nice day, 

Sonia Aguilera
PhD Student
ENSCM

> 
> Message: 2
> Date: Wed, 5 Jul 2017 17:47:08 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Acetonitrile
>   with CHARMM ff
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> 
> 
> On 7/5/17 10:47 AM, Sonia Milena Aguilera Segura wrote:
> >> On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote:
> >>> Dear GROMACS users,
> >>>
> >>> I am currently interested in studying properties of some solvents, among
> >>> them acetonitrile and isopropanol. I would like to use CHARMM force field
> >>> for compatibility with other molecules and I am taking my initial
> >>> structure files from virtualchemistry.org. Does someone know how to run
> >>> the 6-sites model available with the CHARMM ff in gromacs? As I try to
> >>> run
> >>> the simulation box I get the error "No Defaul Proper Dih. Types". I
> >>> checked the ffbonded file and I didn't see the dihedrals defined as in
> >>> the
> >>> rtp file. And for what I've understood this is
> >>
> >> Dihedrals aren't required in .rtp files since pdb2gmx generates them.
> > 
> > 
> > Dear Justin,
> > 
> > Thank you for the comments. Yes, sorry, I was referring to the top file
> > generated by pdb2gmx instead of the rtp file. The top file has the
> > dihedrals defined whereas ffbonded files does not.
> > 
> > 
> >>
> >> because acetonitrile is a linear molecule and dihedrals for three colinear
> >> atoms
> >> this are mathematically
> >>
> >> There are still H-C-C-N dihedral terms.
> > 
> > 
> > Yes, they are named in the top file but not really defined in the ffbonded
> > file, which is why I get the error.
> > 
> 
> pdb2gmx will blindly generate all possible dihedrals; sometimes this isn't
> right.
> 
> It even appears that such parameters (H-C-C-N) do not exist in any CHARMM
> force
> field file.  Perhaps it's meant that way, but I have never tried to simulate
> anything with it.
> 
> > 
> >>
> >> undefined. Also, when I go to check the available itp for acetonitrile in
> >> virtualchemistry.org, I can see that there is a 7-sites model,with a dummy
> >> atom
> >> included. However, for this case, pdb and itp files do not match. I have
> >> seen
> >> that this can be sort of solved by fixing the angle as 179.9, but I really
> >> don't
> >> exactly what to change
> >>> or where in the force field files. I have no experience modifying
> >>> force
> >>> fields. Also, I've seen that for
> >>
> >> Don't modify the force field.  The CHARMM parameters for acetonitrile were
> >> generated in CHARMM, which can handle linear angles without the tricks
> >> that
> >> GROMACS requires with virtual sites.
> > 
> > 
> > So, what you are saying is that it is not possible to simulate the 6-sites
> > model of acetonitrile in GROMACS using CHARMM?
> 
> Never tried it.  AFAIK, GROMACS needs special treatment for linear species.
> Hopefully someone who has actually done such a simulation will say something,
> because my usefulness here is at its end :)
> 
> -Justin
> 
> > 
> >>
> >> the opls ff both pdb and itp files match, but I really need to use the
> >> CHARMM
> >> force field. Are the opls parameters compatible with CHARMM? Any advice?
> >>>
> >>
> >> Don't mix and match force fields.
> > 
> > 
> > Then, if I cannot run the 6-sites model, what's 

Re: [gmx-users] re cant login to Gromacs User forum

[Mark Abraham]

Hi,

Apologies, I meant that last email to go to Anna only. I've changed that
password ;-)

Mark

On Thu, Jul 6, 2017 at 10:37 AM Mark Abraham 
wrote:

> Hi Anna,
>
> I assume you meant logging into http://www.gromacs.org/. I made you an
> account in the name alohn...@bond.edu.au with password "gromacs." Please
> log in and change at least the password.
>
> If you meant something else, can you let me know?
>
> Mark
> On Thu, Jul 6, 2017 at 10:30 AM Anna Lohning  wrote:
>
>> Hi
>>
>> I'm having all kinds of trouble logging in to the Gromacs User Forum. I
>> have registered but when I try to log in with my email (assuming this is my
>> 'username') and password it says there's no user by that name.
>> It's super frustrating. Is there a problem with the site?
>>
>> Would appreciate any help.
>>
>> THanks
>>
>>
>> Kind regards
>>
>> Anna
>>
>>
>> Dr Anna Elizabeth Lohning
>> Assistant Professor - Biochemistry
>> Faculty of Health Science & Medicine
>> Bond University
>> ROBINA 4229
>> (07) 5595 4779
>> alohn...@bond.edu.au
>> --
>> 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.
>>
>
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Re: [gmx-users] Fwd: Relative free energy perturbation

[Hannes Loeffler]

On Thu, 6 Jul 2017 09:17:18 +0200
Davide Bonanni  wrote:

> I am apologize if I resend the same message but I forgot to change the
> object.
> 
> Dear Hannes,
> 
> Thank you very much for your reply, really appreciated.
> 
> 
> 
> > Date: Mon, 26 Jun 2017 12:09:45 +0100
> > From: Hannes Loeffler 
> > To: 
> > Cc: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> > Message-ID: <20170626120945.75215...@stfc.ac.uk>
> > Content-Type: text/plain; charset="US-ASCII"
> >
> > On Mon, 26 Jun 2017 12:25:19 +0200
> > Davide Bonanni  wrote:
> >  
> > > 1) Can I perform the calculation in a single step with soft core
> > > potential enabled? I mean, is it correct to transform directly the
> > > hydrogen into a chlorine instead of using 2 topologys and 2
> > > complexes, where in the first step I transform the hydrogen into
> > > dummy atom, and in the second I transform the dummy atom into
> > > chlorine.  
> >
> > Technically speaking you can perfectly do that but in practice it
> > can be much more efficient to directly and linearly transform one
> > atom type into another (single topology approach).  There is no
> > need for a softcore potential in this case.  Those would only be
> > activated for atoms that either appear or disappear i.e. atoms with
> > zero vdW parameters.  The input and topology files from FEsetup
> > should be all you need.  
> 
> 
> Can I have problems if I keep active the softcore potential whether
> is not needed?

I don't think vdW softcores would be activated as said above. In any
case you can just sc-alpha=0 to switch softcores off all together.
Even if they were on, all that would happen is that you would choose an
alternative path (so need to be consistently used in the other leg(s)
of the thermodynamic cycle).  So you should get the same overall ddG
albeit in a possible less efficient fashion because you completely
decouple on atom while recoupling its counter-part.  It just doesn't
make sense to me to do it that way.

Cheers,
Hannes.
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Re: [gmx-users] re cant login to Gromacs User forum

[Mark Abraham]

Hi Anna,

I assume you meant logging into http://www.gromacs.org/. I made you an
account in the name alohn...@bond.edu.au with password "gromacs." Please
log in and change at least the password.

If you meant something else, can you let me know?

Mark

On Thu, Jul 6, 2017 at 10:30 AM Anna Lohning  wrote:

> Hi
>
> I'm having all kinds of trouble logging in to the Gromacs User Forum. I
> have registered but when I try to log in with my email (assuming this is my
> 'username') and password it says there's no user by that name.
> It's super frustrating. Is there a problem with the site?
>
> Would appreciate any help.
>
> THanks
>
>
> Kind regards
>
> Anna
>
>
> Dr Anna Elizabeth Lohning
> Assistant Professor - Biochemistry
> Faculty of Health Science & Medicine
> Bond University
> ROBINA 4229
> (07) 5595 4779
> alohn...@bond.edu.au
> --
> 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.
>
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Re: [gmx-users] re cant login to Gromacs User forum

[Mark Abraham]

Hi Anna,

I'm not sure what forum you're referring to. www.gromacs.org is currently
under replacement, in part because such things do not work well and the
infrastructure is out of supported lifetime. I'll contact you off-list for
some details.

Mark

On Thu, Jul 6, 2017 at 10:30 AM Anna Lohning  wrote:

> Hi
>
> I'm having all kinds of trouble logging in to the Gromacs User Forum. I
> have registered but when I try to log in with my email (assuming this is my
> 'username') and password it says there's no user by that name.
> It's super frustrating. Is there a problem with the site?
>
> Would appreciate any help.
>
> THanks
>
>
> Kind regards
>
> Anna
>
>
> Dr Anna Elizabeth Lohning
> Assistant Professor - Biochemistry
> Faculty of Health Science & Medicine
> Bond University
> ROBINA 4229
> (07) 5595 4779
> alohn...@bond.edu.au
> --
> 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.
>
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[gmx-users] re cant login to Gromacs User forum

[Anna Lohning]

Hi

I'm having all kinds of trouble logging in to the Gromacs User Forum. I have 
registered but when I try to log in with my email (assuming this is my 
'username') and password it says there's no user by that name.
It's super frustrating. Is there a problem with the site?

Would appreciate any help.

THanks


Kind regards

Anna


Dr Anna Elizabeth Lohning
Assistant Professor - Biochemistry
Faculty of Health Science & Medicine
Bond University
ROBINA 4229
(07) 5595 4779
alohn...@bond.edu.au
-- 
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Re: [gmx-users] TIP4P/ice pdb file

[G R]

Dear Chris,

Yes, tip4p.gro worked well.

Thank you

On Wed, Jul 5, 2017 at 10:55 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. TIP4P/ice pdb file (G R)
>2. Re: simulation at different temperature (Alex)
>3. Re: simulation at different temperature (Alex)
>4. Re: TIP4P/ice pdb file (Christopher Neale)
>5. Re: TIP4P/ice pdb file (Christopher Neale)
>
>
> --
>
> Message: 1
> Date: Wed, 5 Jul 2017 21:57:26 +0300
> From: G R 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] TIP4P/ice pdb file
> Message-ID:
> 

Re: [gmx-users] Fwd: Relative free energy perturbation

[Davide Bonanni]

I am apologize if I resend the same message but I forgot to change the
object.

Dear Hannes,

Thank you very much for your reply, really appreciated.



> Date: Mon, 26 Jun 2017 12:09:45 +0100
> From: Hannes Loeffler 
> To: 
> Cc: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> Message-ID: <20170626120945.75215...@stfc.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Mon, 26 Jun 2017 12:25:19 +0200
> Davide Bonanni  wrote:
>
> > 1) Can I perform the calculation in a single step with soft core
> > potential enabled? I mean, is it correct to transform directly the
> > hydrogen into a chlorine instead of using 2 topologys and 2
> > complexes, where in the first step I transform the hydrogen into
> > dummy atom, and in the second I transform the dummy atom into
> > chlorine.
>
> Technically speaking you can perfectly do that but in practice it can
> be much more efficient to directly and linearly transform one atom type
> into another (single topology approach).  There is no need for a
> softcore potential in this case.  Those would only be activated for
> atoms that either appear or disappear i.e. atoms with zero vdW
> parameters.  The input and topology files from FEsetup should be all
> you need.


Can I have problems if I keep active the softcore potential whether is not
needed?


> > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> > x-tutorials/free_energy/index.html), I have to perform every step of
> > molecular dynamics at every Lambda value, is that right?
>
> Yes, you will need to do a simulation for every and each lambda step.
>
>
> > 3) I run a test minimization step (mdp file attached) of my complex
> > at the last "init-lambda-state", 15 in my case. Looking at the .trr
> > output file I can see that the bond between the carbon and the
> > hydrogen which should be trasformed is longer than a normal C-H bond,
> > but the atom is still recognized as hydrogen (picture
> > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> > blue -> init-lambda-state = 15). I was wondering if this is what I am
> > supposed to see, so if gromacs is considering the state B of my
> > system where I have chlorine bound to carbon instead hydrogen.
>
> What does "recognized as hydrogen" mean?  I suspect that what you are
> referring to is the output of some visualisation program because you
> instructed it to interpret that particular atom to be a hydrogen.
>
> What you need to expect to see is that a C-H bond is transformed into a
> C-Cl bond and accordingly the bond length increases.
>

Of course, It's like you said. I see the bond length increase as in the img
"http://tinypic.com/r/2wp11dh/9;.
Thank you again.

Cheers,

Davide Bonanni
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