[gmx-users] there are fewer frames in your trajectory than there are degrees of freedom in your system.

[venkat]

Dear gromacs users,
i tried to analysis trajectory using covar
command (gmx_mpi covar -s *prot_only-apo.pdb *-f *PROTEIN.xtc* -v
eigenvect.trr -xpma covara.xpm)
 i got following warning
*WARNING: there are fewer frames in your trajectory than there are degrees
of freedom in your system. Only generating the first 400 out of 3564
eigenvectors and eigenvalues.*

 kindly provide suggestions weather can i ignore above mentioned warning or
not

thank you
venkat
-- 
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] Regarding calculation of SDF

[Dilip.H.N]

Hello,
Hoping for a positive response...

Thank you.



[image: Mailtrack]

Sender
notified by
Mailtrack

05/31/18,
9:26:54 AM

---
With Best Regards,

Dilip.H.N
PhD Student.

On Mon, May 28, 2018 at 7:47 AM, Dilip.H.N 
wrote:

> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and
> all the oxygen atoms of water molecules. And here are my commands that i
> gave inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur
> compact -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit
> rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-
> 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298
> TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-
> 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298
> Last frame  6 time 3.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper
> SDF/it is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> 
>  Sender
> notified by
> Mailtrack
> 
>  05/28/18,
> 7:47:09 AM
>
-- 
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] Virtual sites causing npt simulation instabilities

[Dallas Warren]

Always good practice to use Berendsen when turning on constant
pressure first, it is much more robust than P-R.  Let that run for
awhile, let it equilibrate, then turn on P-R.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 31 May 2018 at 06:40, Eisenhart, Andrew (eisenhaw)
 wrote:
> Hello all,
>
> I am having an issue with the current systems I am working on. The system 
> consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and 
> hw2; and 3 massless point charges for the electrostatics). The three point 
> charges I have implemented as virtual interaction sites using the section 
> below in my topology file.
>
>
> [ virtual_sites3 ]
> ; Vsite fromfunct   a   b
> 4   1   2   3   1   0.29869481802   0.29869481802
> ; Vsite (3fad) functtheta   d
> 5   3   2   1   3 18.060.025
> 6   2   3   1   3 18.060.025
>
>
> this is loosely based on the tip4p model. Since the two partial charges off 
> of the hydrogens differ only in location I have them defined as a single type 
> with sigma and epsilon defined as 0. I have also done this to the partial 
> charge off of the oxygen. This is all seen below in my atomtypes and atoms 
> sections.
>
>
> [ atomtypes ]
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>   qm1   qm1 0.000   -2.516A  0.000  0.000
>   qh1   qh1 0.0001.258A  0.000  0.000
>
> ---
>
> [ atoms ]
> ; idat type res nr  residu name at name cg nr   charge
> 1   opls_1131   M3  OW 1   0.0
> 2   opls_1141   M3 HW1 1   0.0
> 3   opls_1141   M3 HW2 1   0.0
> 4   qm1 1   M3  qm 1  -2.516
> 5   qh1 1   M3 qh1 1   1.258
> 6   qh1 1   M3 qh2 1   1.258
>
> The problem I am seeing right now depends on the parameters I use in the mdp 
> files. During thermostat equlibration nothing is amiss, but once the volume 
> of the box is allowed to relax the problems show. Using the parrinello-rahman 
> barostat and 0.002fs timestep I crash with lincs warnings. Reducing the 
> timestep to 0.001fs stops the lincs warnings, but the box size never 
> converges It  instead expands to around 10x its original size. So I think 
> that I must have a problem with the implementation of my virtual sites. Any 
> guidance would be greatly appreciated. Thanks below are some other parameters 
> I have set in my input files.
>
> Andrew
>
>
> integrator  =  md
> nsteps  =  50
> nstcomm =  100
> nstxout =  0
> nstvout =  0
> nstfout =  0
> nstlog  =  1000
> nstenergy   =  1000
> nstxtcout   =  1000
> nstlist =  5
> ns_type = grid
> pbc =  xyz
> coulombtype = pme
> rcoulomb= 0.5
> rlist   = 0.5
> vdw-type= cut-off
> rvdw=0.5
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter  = 1
> lincs_order = 8
> fourierspacing   = 0.10
> pme_order= 6
> ewald_rtol   = 1e-06
> ewald_geometry   = 3d
> optimize_fft = yes
> tcoupl  = Nose-Hoover
> tc-grps = System
> tau_t   = 0.4
> ref_t   = 300
> ; Pressure coupling is on
> pcoupl  = parrinello-rahman
> pcoupltype  = isotropic
> tau_p   = 2.0
> ref_p   = 1.0
> compressibility = 4.5e-5
> refcoord-scaling = com
> DispCorr= EnerPres
> comm-mode   = linear
>
>
>
> --
> 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] rdf at contact

[Dallas Warren]

How noisy is the rdf i.e. what is the bin width, how many atoms etc?
Have you graphed the entire function?  That would be my first
suggestion of the cause.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 31 May 2018 at 00:45, Faezeh Pousaneh  wrote:
> Hi,
>
> I have a system of similar molecules, I would like to obtain the rdf at
> contact (meaning, at surface of one particle).
> What I try is; I make an index file containing only central atoms of all
> molecules, then I run:
>
>
> gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b
>  14000
>
> ref 0 is a single atom
> ref 1 is rest of atoms
>
>
> Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
> file.
> My problem is I get very different values  for different time intervals
> (after equilibrium) . Why is that so?
>
> I appreciate if sb can help.
> Best regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

[Seyed Mojtaba Rezaei Sani]

 Dear all,

I am trying to calculate the order parameter of lipid acyl chains in a
bilayer surrounding a drug molecule using Gromacs. To do this, I defined
four regions in the bilayer: two local regions within a considered shell in
the x-y plane around the drug (one for the leaflet containing the drug and
the other for the opposite one) and two global regions beyond the shell.
My problem is that how to find lipid molecules which are located in the
local shell in order to make an index group of their carbon chains for
calculation of order parameter. Is there any Gromacs' tool for such
calculation?

Best regards,


-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)
-- 
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] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Hello all,

I am having an issue with the current systems I am working on. The system 
consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and 
hw2; and 3 massless point charges for the electrostatics). The three point 
charges I have implemented as virtual interaction sites using the section below 
in my topology file.


[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025


this is loosely based on the tip4p model. Since the two partial charges off of 
the hydrogens differ only in location I have them defined as a single type with 
sigma and epsilon defined as 0. I have also done this to the partial charge off 
of the oxygen. This is all seen below in my atomtypes and atoms sections.


[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
  qm1   qm1 0.000   -2.516A  0.000  0.000
  qh1   qh1 0.0001.258A  0.000  0.000

---

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258

The problem I am seeing right now depends on the parameters I use in the mdp 
files. During thermostat equlibration nothing is amiss, but once the volume of 
the box is allowed to relax the problems show. Using the parrinello-rahman 
barostat and 0.002fs timestep I crash with lincs warnings. Reducing the 
timestep to 0.001fs stops the lincs warnings, but the box size never converges 
It  instead expands to around 10x its original size. So I think that I must 
have a problem with the implementation of my virtual sites. Any guidance would 
be greatly appreciated. Thanks below are some other parameters I have set in my 
input files.

Andrew


integrator  =  md
nsteps  =  50
nstcomm =  100
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  1000
nstenergy   =  1000
nstxtcout   =  1000
nstlist =  5
ns_type = grid
pbc =  xyz
coulombtype = pme
rcoulomb= 0.5
rlist   = 0.5
vdw-type= cut-off
rvdw=0.5
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter  = 1
lincs_order = 8
fourierspacing   = 0.10
pme_order= 6
ewald_rtol   = 1e-06
ewald_geometry   = 3d
optimize_fft = yes
tcoupl  = Nose-Hoover
tc-grps = System
tau_t   = 0.4
ref_t   = 300
; Pressure coupling is on
pcoupl  = parrinello-rahman
pcoupltype  = isotropic
tau_p   = 2.0
ref_p   = 1.0
compressibility = 4.5e-5
refcoord-scaling = com
DispCorr= EnerPres
comm-mode   = linear



-- 
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] Install Gromacs Cuda MacBook pro with eGPU OS X 10.13.4

[Владимир Богданов]

  Hey! Maybe somewhere could help me. I have some problems when I try to compile gromacs on OS X with eGPU: Copyright (c) 2005-2017 NVIDIA CorporationBuilt on Tue_Dec_19_21:36:29_CST_2017Cuda compilation tools, release 9.1, V9.1.128 when I use clang/clang++ compilers: clang -vclang version 6.0.0 (tags/RELEASE_600/final)Target: x86_64-apple-darwin17.5.0Thread model: posixInstalledDir: /usr/local/Cellar/llvm/6.0.0/binFound CUDA installation: /usr/local/cuda, version unknownI can found OpenMP:-- Found OpenMP_C: -fopenmp=libomp (found version "3.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1")  but:-- Check for working NVCC/C compiler combination-- Check for working NVCC/C compiler combination - brokenCMake Error at cmake/gmxManageGPU.cmake:291 (message):  CUDA compiler does not seem to be functional.  -- Configuring incomplete, errors occurred! when I use   llvm-gcc/llvm-g++ or CC/C++ compilers: c++ -vApple LLVM version 9.0.0 (clang-900.0.39.2)Target: x86_64-apple-darwin17.5.0Thread model: posixInstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/binFound CUDA installation: /usr/local/cuda, version unknown llvm-gcc -vApple LLVM version 9.0.0 (clang-900.0.39.2)Target: x86_64-apple-darwin17.5.0Thread model: posixInstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/binFound CUDA installation: /usr/local/cuda, version unknown I can not find OpenMP: -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) (found version "1.0")-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) (found version "1.0") and when I do make: [  3%] Building C object src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o[  3%] Built target tng_io_obj[  3%] Generating baseversion-gen.c[  3%] Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o/Users//Downloads/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_pruneonly.cu(41): error: explicit instantiation definition directive for __global__ functions with clang host compiler is not yet supported /Users//Downloads/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_pruneonly.cu(42): error: explicit instantiation definition directive for __global__ functions with clang host compiler is not yet supported 2 errors detected in the compilation of "/var/folders/ls/_pffbhc9613d67c9jh2jhbyrgn/T//tmpxft_0001457e_-13_nbnxn_cuda.compute_70.cpp1.ii".CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:282 (message):  Error generating file  /Users//Downloads/gromacs-2018.1/build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o  make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o] Error 1make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2 -- Thanks,Vlad-- 
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] Confusing gmx tMPI Error

[Mark Abraham]

Hi,

That sounds like a bug worth looking into. If you can open an issue at
https://redmine.gromacs.org/ and upload your inputs to grompp and mdrun and
the output (particularly the .log fie), then we can see if we can reproduce
the problem and find a fix.

Mark

On Wed, May 30, 2018 at 8:41 PM William Barber 
wrote:

> Hello, I have a system which I'm trying to simulate. I can get it to run on
> some systems with GPU or CPU just fine, and on one system which was working
> fine with Gromacs a few days ago I can only run it on the CPU. If I run it
> on the two GPUs in the system I get this error:
>
> Wrote pdb files with previous and current coordinates
> tMPI error: Receive buffer size too small for transmission (in valid comm)
> Aborted (core dumped)
>
> Clearly onl the tMPI line is truly relevant here. It's a very confusing
> error to receive, and I've been unable to find anything on the web
> regarding this error. The system functions fine on other systems on one or
> more GPUs or on any systems CPU, so I can only assume it has something to
> do with the GPUs on this system despite them working just fine a couple of
> days ago. The only "errors" before that are LINCS warnings, which I expect
> to see during this energy minimization process.
>
> To rule out it being a damaged install of Gromacs I've also gone and
> deleted and recompiled from scratch a clean copy of Gromacs 2016.4. Any
> suggestions on how I can better diagnose or solve this problem would be
> greatly appreciated! Thanks,
>
> Will
> University of Ontario Institute of Technology
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Confusing gmx tMPI Error

[William Barber]

Hello, I have a system which I'm trying to simulate. I can get it to run on
some systems with GPU or CPU just fine, and on one system which was working
fine with Gromacs a few days ago I can only run it on the CPU. If I run it
on the two GPUs in the system I get this error:

Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid comm)
Aborted (core dumped)

Clearly onl the tMPI line is truly relevant here. It's a very confusing
error to receive, and I've been unable to find anything on the web
regarding this error. The system functions fine on other systems on one or
more GPUs or on any systems CPU, so I can only assume it has something to
do with the GPUs on this system despite them working just fine a couple of
days ago. The only "errors" before that are LINCS warnings, which I expect
to see during this energy minimization process.

To rule out it being a damaged install of Gromacs I've also gone and
deleted and recompiled from scratch a clean copy of Gromacs 2016.4. Any
suggestions on how I can better diagnose or solve this problem would be
greatly appreciated! Thanks,

Will
University of Ontario Institute of Technology
-- 
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] Problem with constrains and degrees of freedom

[Sergi Ruiz Barragán]

I want to reproduce the simulations done by Luis et al in 
10.1021/acsnano.7b06805 , where they use a rigid graphene layers. I'm 
using constraints to keep the graphene sheet in a plane. However, I'm 
not sure if the degree of freedom are ok. In fact, I don't know where to 
check how many degrees of freedom are gromacs considering. In this case, 
when the graphene is simulated as a rigid lamina , it has a unique 
degree of freedom (up/down in the axis perpendicular to the sheet). 
However, I think this is not taking care by gromacs.


--
Sergi Ruiz Barragán
Lehrstuhl für Theoretische Chemie - Center for Theoretical Chemistry
Ruhr-Universität Bochum (RUB) - University of Bochum
Universitätsstraße 150, 44801 Bochum (Germany)
Tel: +49 (0)234 32 28081

--
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] Restrain on principal axis to inhibit protein rotation

[Soeren von Buelow]

Dear all,

I would like to simulate an elongated ('stretched-out', rod-like)
protein in an orthorhombic or tetragonal box to simulate as few solvent
particles as possible and save computation time. The longest axis of the
protein would be aligned to the box axis with largest side-length.

The problem that I have with this approach is that the protein
(obviously) tends to rotate and see its periodic images, once the
longest axes of protein and box are no longer aligned. I'm not
interested in the rotational diffusion of the protein, so I'm fine with
imposing a soft collective restraint on the orientation of the protein
to keep it from rotating.

I don't want to restrain each atom individually, because that would mess
up the dynamics of the protein, but would rather like to impose an
energy penalty (harmonic or flat-bottom potential or anything actually),
if the vector of the largest principal axis of the inertia tensor
deviates by too much from the starting structure. This would allow
internal fluctuations to continue happily, as long as the protein does
not rotate too much globally.

Do you have any idea how to do that in gromacs? I only found an
implementation in a hacked older gromacs version from this paper

dx.doi.org/10.1021/ct100666v | J. Chem. Theory Comput. 2011, 7, 1381–1393,

but I would like to stick with some of the recent gromacs implementations.

Thanks and best regards,

-- 
Sören
-- 
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] rdf at contact

[Faezeh Pousaneh]

Hi,

I have a system of similar molecules, I would like to obtain the rdf at
contact (meaning, at surface of one particle).
What I try is; I make an index file containing only central atoms of all
molecules, then I run:


gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b
 14000

ref 0 is a single atom
ref 1 is rest of atoms


Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
file.
My problem is I get very different values  for different time intervals
(after equilibrium) . Why is that so?

I appreciate if sb can help.
Best regards
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gmx conver-tpr error

[Amali Guruge]

Dear Dr. Justin,

Thank you very much for the reply.
I'm sure, I used -extend for the gmx convert-tpr.

How can I solve this problem?
Appreciate, if you could help me.
Thank you.


On Wed, May 30, 2018 at 9:51 PM, Justin Lemkul  wrote:

>
>
> On 5/30/18 5:51 AM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
>> Therefore, I used the command,
>> gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
>> But I got the error, 'You've simulated long enough. Not writing tpr file.'
>>
>> How can I solve the problem?
>>
>
> Are you sure that was your exact command? You didn't accidentally type
> "-until" rather than "-extend" in your command? Any use of -extend
> shouldn't trigger that error, but -until would do exactly that in this
> instance.
>
> -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.

[gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

[Seyed Mojtaba Rezaei Sani]

Dear all,

I am trying to calculate the order parameter of lipid acyl chains in a
bilayer surrounding a drug molecule using Gromacs. To do this, I defined
four regions in the bilayer: two local regions within a considered shell in
the x-y plane around the drug (one for the leaflet containing the drug and
the other for the opposite one) and two global regions beyond the shell.
My problem is that how to find lipid molecules which are located in the
local shell in order to make an index group of their carbon chains for
calculation of order parameter. Is there any Gromacs' tool for such
calculation?

Best regards,


-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)
-- 
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] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

[zeineb SI CHAIB]

Dear all,


Thank you for your suggestions and help.


@Quyen, I checked the energies, box fluctuations and pressure deviations and 
everything seem correct: Energies (potential, kinetic and total) were stable 
during the simulation and the average of the pressure was 1.04 bar.


@ Peter, I equilibrated my system for 50ns (NPT equilibration followed by NVT 
equilibration, both during 50ns each one). Also, the system crashed after 2.5 
μs of simulation.


@ Kevin,  I run the simulation with the option -rdd 1.5 but the system crashed 
in the same step with the same error: Fatal error: bond length not finite. I 
also noticed that before crashing, I had too many LINCS warning!


I still don't see where could be the problem, especially that everything was 
good for 2.5μs of simulation...



Best,


Zeineb

-- 
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] md simulation of oil hydrocarbon / L-OPLS

[Smith, Micholas D.]

Hydrocarbons with less than 200 atoms can be generate from the server I 
mentioned. For larger hydrocarbons, it would be best to develop smaller 
residues ( say C8 through C16 ) and stitch them together to form the larger 
hydrocarbons and then validate the models/tune the parameters as necessary. 
This in itself is a fairly massive undertaking since you would essentially be 
making a new force-field (similar to how protein force-fields were developed). 
That being said, it would be immensely useful.

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Atila 
Petrosian 
Sent: Tuesday, May 29, 2018 9:29 PM
To: gmx-users
Subject: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Micholas,

I have many hydrocarbons (small to large) for study,  C8 - C50, .
--
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] gmx conver-tpr error

[Justin Lemkul]

On 5/30/18 5:51 AM, Amali Guruge wrote:

Dear Gromacs users,

I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
Therefore, I used the command,
gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
But I got the error, 'You've simulated long enough. Not writing tpr file.'

How can I solve the problem?


Are you sure that was your exact command? You didn't accidentally type 
"-until" rather than "-extend" in your command? Any use of -extend 
shouldn't trigger that error, but -until would do exactly that in this 
instance.


-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] topology

[Justin Lemkul]

On 5/29/18 3:39 PM, mostafa paknia wrote:

you said "The drug topology (.itp) can then be #included

within the .top file generated for the CNT.
"
?but how
that's Complicated for me
I need more help if it's possible for you


I suggest with learning to handle simpler systems first. Learn how to 
make the CNT topology and make sure you can simulate that. Study the 
GROMACS manual and tutorials to learn about topology format, contents, 
and manipulation. Learn to walk before you run - what you're trying to 
do is complex and is certainly prone to mistakes if you don't know what 
you're doing.


-Justin


2018-05-29 22:41 GMT+03:30 Justin Lemkul :


On 5/29/18 3:08 PM, mostafa paknia wrote:

Hi
I have two topology files already
One of them is CNT's topology & otherone is a drug topology
I want to make them just one
How can i do that


I already answered this a few days ago:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-May/120487.html

-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

==



--
==

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] How to define a vector for gangle command

[Justin Lemkul]

On 5/30/18 4:06 AM, delara aghaie wrote:

Dear Gromacs users
My simulation box contains dppc lipid bilayer containing a membrane protein.
I want to calculate the angle between P-N in dppc head group and the bilayer 
normal (z-axis).
We want to use the gromacs gangle command for this purpose.

The command asks us to define a vector for P-N, while for the axis z it does 
not require vector definition.
I can make an index group containing all the P and N atoms of the dppc 
headgroup, but I do not know how to make a vector from these two endpoints to 
give it to the gangle command for angle calculation.


Use gmx gangle -g2 z

-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] gmx conver-tpr error

[Soham Sarkar]

tpbconv -s md.tpr -o md_new.tpr -extend 5

On Wed, 30 May 2018, 3:22 pm Amali Guruge,  wrote:

> Dear Gromacs users,
>
> I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
> Therefore, I used the command,
> gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
> But I got the error, 'You've simulated long enough. Not writing tpr file.'
>
> How can I solve the problem?
>
> Thank you.
>
> 
>
> 
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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] gmx conver-tpr error

[Amali Guruge]

Dear Gromacs users,

I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
Therefore, I used the command,
gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
But I got the error, 'You've simulated long enough. Not writing tpr file.'

How can I solve the problem?

Thank you.




-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] How to define a vector for gangle command

[delara aghaie]

Dear Gromacs users
My simulation box contains dppc lipid bilayer containing a membrane protein.
I want to calculate the angle between P-N in dppc head group and the bilayer 
normal (z-axis).
We want to use the gromacs gangle command for this purpose.

The command asks us to define a vector for P-N, while for the axis z it does 
not require vector definition.
I can make an index group containing all the P and N atoms of the dppc 
headgroup, but I do not know how to make a vector from these two endpoints to 
give it to the gangle command for angle calculation.

Your help would be greatly appreciated.
Best regards
Delara
-- 
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] backbone contact analysis of martini cg protein

[Alex]

Some respect for this user board would be nice.

If there is anything unclear about how gmx make_ndx works, please ask a 
specific question instead of posting the same very unclear thing over 
and over. Noone will be able to help with your question, because it 
requires precise knowledge of your system and what must be included in 
the index to calculate what you need. You're basically asking others to 
do your job for you.


Alex


On 5/29/2018 11:49 PM, SHAHEE ISLAM wrote:

can anyone please give me some idea.

On 5/30/18, SHAHEE ISLAM  wrote:

hi,
i want to calculate the contact between the backbone of protein(it is
a coarse grained protein using martini force field).how i will make
.ndx file to calculate the contact.

thanking you
shahee islam
university of calcutta



--
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.