from:"Neena Susan Eappen"

[gmx-users] Opening PDB files in GROMACS on Windows using Cygwin

2018-11-02 Thread Neena Susan Eappen

Hello GROMACS users,


I am a first time user of GROMACS. According to this excellent tutorial 
(http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the PDB 
file for lyzozyme, then removed water molecules, typed in the following command 
on CygwinShell (with GROMACS activated).

$ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce

However, I get an error saying:

In command line option -f, file 1AKI_clean.pdb does not exit or is not 
accessible.

Please advice where am I going wrong. Any insight would be appreciated.

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab, U of T
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Re: [gmx-users] Opening PDB files in GROMACS on Windows using Cygwin

2018-11-02 Thread Neena Susan Eappen

Thank you Benson Muite and Bratin Kumar for replying. I am using version 5.1.1. 
Thanks Bratin for pointing that out, now it works when the file was transferred 
to the working directory!


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Today's Topics:

   1. Re: Gmx distance (rose rahmani)
   2. Opening PDB files in GROMACS on Windows using Cygwin
  (Neena Susan Eappen)
   3. Re: Opening PDB files in GROMACS on Windows using Cygwin
  (Benson Muite)
   4. Re: Opening PDB files in GROMACS on Windows using Cygwin
  (Bratin Kumar Das)


--

Message: 1
Date: Fri, 2 Nov 2018 19:06:36 +0330
From: rose rahmani 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gmx distance
Message-ID:

Content-Type: text/plain; charset="UTF-8"

but this is output of -oall. its not a single value?!

  gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
# gmx distance is part of G R O M A C S:
#
#
??<8d><9a><9a><91>???<9a><9b>???<8d><9e><91><98><9a>???<9e><98><9a><91><8b><9e>???<85><8a><8d><9a>???<86><9e><91>???<94><86><9d><99a>8a><<
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy

1.0000.2290.2290.4460.5820.4460.2290.446
0.5830.4470.2290.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2270.2280.4460.5820.4460.2270.446
0.5830.4470.2270.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4470.2270.2290.2290.446
0.5820.4460.2290.4460.5830.4470.2290.447
0.2270.2290.2290.4460.5820.4460.2290.446
0.5830.4470.2290.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4470.2270.2270.2280.446
0.5820.4460.2270.4460.5830.4470.2270.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4
.
.
.

and this is -o of g_dist;
 g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
#
# g_dist is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
   0.0000.2176011   -0.0120678   -0.04654980.2122209
   1.0000.2124534   -0.0301750   -0.04638700.2051198
   2.0000.1923753   -0.0158403   -0.05101350.1848106
   3.0000.1885315   -0.0107298   -0.04881600.1817856
   4.0000.2044982   -0.0052650   -0.04903290.1984630
   5.0000.2033602   -0.0002742   -0.04295370.1987720
   6.0000.20504870.0013833   -0.04446580.2001646
   7.0000.20024750.0041072   -0.04150030.1958568
   8.0000.20064730.0033450   -0.05118890.1939790
   9.0000.2032918   -0.119   -0.03300520.2005947
  10.0000.22556590.0003929   -0.04158570.2216990
  11.0000.22438110.0118313   -0.03447510.2214010
  12.0000.23478550.0078275   -0.03835320.2314994
  13.0000.23715410.0081918   -0.03882670.2338107
.
.
.


On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul  wrote:

>
>
> On 11/1/18 2:25 PM, rose rahmani wrote:
> > I do

[gmx-users] Vacuum simulation of a peptide feasible using GROMACS?

2018-11-09 Thread Neena Susan Eappen

Hello GROMACS users,


I am a first time user of GROMACS. I was wondering can I model a peptide (to 
learn about secondary structure) in gas phase with different charge sites using 
GROMACS?


Many thanks,


Neena Eappen
Graduate Student
Jockusch Lab, U of T
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[gmx-users] Input file for energy minimization for solvated system: Error

2018-11-11 Thread Neena Susan Eappen

Hello GROMACS users,


I was trying to create an input file for energy minimization of solvated 
system, using the following command:

grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o 
protein-EM-solvated.tpr

Got the following error:
number of coordinates in coordinate file (1y6l-solvated.gro, 181577) does not 
match topology (1y6l.top, 182265).

I think the following error occurred because I skipped the following step:
Edit the topology file and decrease the number of solvent molecules. Also add a 
line specifying the number of NA ions and a line specifying the amount of CL.

My question:

  1.  How to open the topology file?
  2.  How do I determine number of NA and CL ions added? I just saw a massive 
list of these counterions being added, but not the total number.
  3.  My net charge on the protein was 6+, why do I need to add Na+ ions?

Any insight would be appreciated, Thank you,


Neena Eappen
Graduate Student
Jockusch Lab, U of T
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[gmx-users] Error: Cannot set thread affinities on the current platform

2018-11-11 Thread Neena Susan Eappen

Hello GROMACS users,


I am running GROMACS version 5.1.1 on windows using cygwin (latest 
version).After the following command: gmx mdrun -deffnm nvt

Error message: Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 
on this machine, which is better

Reading file nvt.tpr, VERSION 5.1.1 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.029

Using 1 MPI thread
Using 4 OpenMP threads

NOTE: Cannot set thread affinities on the current platform.
starting mdrun 'Protein in water'
5 steps,100.0 ps.

Could there be anything incompatible between Cygwin and Gromacs here? Any 
insight would be appreciated, Many thanks,


Neena Eappen
Graduate Student
Jockusch Lab, U of T
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Re: [gmx-users] Error: Cannot set thread affinities on the current platform

2018-11-23 Thread Neena Susan Eappen

What do these thread affinities refer to?
Does that error have an impact on simulations? My simulations were still 
completed without any halt in between.

Thank you,
Neena
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[gmx-users] Shell platform for GROMACS on Windows?

2019-01-07 Thread Neena Susan Eappen

Hello GROMACS users,


To run GROMACS on Windows OS, what is the best shell interface? Cygwin? or 
anything else?


Thank you,

Neena
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Re: [gmx-users] Shell platform for GROMACS on Windows?

2019-01-08 Thread Neena Susan Eappen

Thank you Wahab,


Is there any issue with using Cygwin on Windows using GROMACS?


Neena



From: Neena Susan Eappen
Sent: Tuesday, January 8, 2019 4:07 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Shell platform for GROMACS on Windows?


Hello GROMACS users,


To run GROMACS on Windows OS, what is the best shell interface? Cygwin? or 
anything else?


Thank you,

Neena
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[gmx-users] Single precision enough for MD of peptide?

2019-01-12 Thread Neena Susan Eappen

Hi GMX users,


I just installed GROMACS 2018.4 on my windows PC without GPU support. My PC is 
capable of only single precision with a 64-bit memory, would this affect the 
trajectory of my peptide?


Many thanks,

Neena
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Re: [gmx-users] Single precision enough for MD of peptide?

2019-01-15 Thread Neena Susan Eappen

Hi Justin,


Thank you. What is the solution for this?


Neena


From: Neena Susan Eappen
Sent: Saturday, January 12, 2019 3:15:11 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Single precision enough for MD of peptide?


Hi GMX users,


I just installed GROMACS 2018.4 on my windows PC without GPU support. My PC is 
capable of only single precision with a 64-bit memory, would this affect the 
trajectory of my peptide?


Many thanks,

Neena
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[gmx-users] pdb2gmx error due to terminal capping of peptide

2019-01-24 Thread Neena Susan Eappen

Hi GMX users,


  1.  I drew the structure of my target peptide on Pymol, added amide capping 
group (NHH) at C terminus of peptide
  2.  Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh
  3.  Chose AMBER99sb-ildn force field which has parameters for NH2 capping 
group
  4.  Fatal error
  5.  Changed naming of amide group in .rtp file of AMBER99sb-ildn from NH2 to 
NHH so that naming is similar to .pdb file.
  6.  Still fatal error.
The residues in the chain ALA16--NHH32 do not have a consistent type. The first 
residue has type 'Protein', while residue NHH32 is of type 'Other'. Either 
there is a mistake in your chain, or it includes nonstandard residue names that 
have not yet been added to the residuetypes.dat file in the GROMACS library 
directory.

Any insight would be appreciated,
Thank you,
Neena
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[gmx-users] Scroll through previous questions

2019-01-27 Thread Neena Susan Eappen

Hi Gromacs users,


Is there a quick way to scroll through previous questions in the mailing list? 
Now, I am able to control find my question of interest only for each month 
separately. Can I look through the entire log file from 2000 till now at once?


Thanks,


Neena Eappen
Graduate Student
Jockusch Lab, U of T
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[gmx-users] PBC conditions for Vacuum simulation

2019-02-09 Thread Neena Susan Eappen

Hello gromacs users,

I am trying to model a peptide in gas phase which requires proper conditions 
like: no PBC, no cut-offs for VanderWaals and electrostatics, coulomb type not 
PME. However, this increases computational time by N^2 for N number of atoms. 
Is there a way to mitigate this?

Many thanks,
Neena

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[gmx-users] Naming convention for Acetyl Terminal group

2019-03-15 Thread Neena Susan Eappen

Hello gromacs users,

A small question, why is that atoms of a methyl group named/ labelled 
differently in an Acetyl terminal group vs Alanine (below parameters from .rtp 
file from OPLS-AA ff)? I do understand naming convention in the methyl group of 
Alanine, but not in acetyl group.

[ ACE ]
 [ atoms ]
   CH3opls_135   -0.180 1
  HH31opls_1400.060 1
  HH32opls_1400.060 1
  HH33opls_1400.060 1
 Copls_2350.500 2
 Oopls_236   -0.500 2

AND

[ ALA ]
 [ atoms ]
 Nopls_238   -0.500 1
 Hopls_2410.300 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_135   -0.180 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
   HB3opls_1400.060 2
 Copls_2350.500 3
 Oopls_236   -0.500 3

Thank you for your knowledge,
Neena
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[gmx-users] Cannot find position restraint file

2019-03-23 Thread Neena Susan Eappen

Hello gromacs users,

For the equilibration phase 1, an error message came up following this command:

gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
Error: Cannot find position restraint file restraint.gro (option -r)

I do not have a posre.gro file, only posre.itp file. I don't understand this, 
any insight would be appreciated.

Thank you,
Neena
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[gmx-users] NVT equilibration in vacuum

2019-03-26 Thread Neena Susan Eappen

Hello gromacs users,

I am using gromacs to simulate a peptide in vacuum. I was wondering for the NVT 
equilibration step, are there any particular parameters to be changed for 
vacuum conditions as there is no position restraining on solvent molecules?

Thank you,
Neena
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[gmx-users] Lowest energy structure after production MD run

2019-04-04 Thread Neena Susan Eappen

Hello gromacs users,

Since the final structure obtained after production MD run is the average 
structure, how to extract out the lowest energy structure?

Thank you for sharing your knowledge,
Neena
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Re: [gmx-users] Lowest energy structure after production MD run

2019-04-05 Thread Neena Susan Eappen

Thank you Dr. Dallas,

I am new to gromacs, so I assumed the final structure was average after 
searching on google.

Neena





From: Neena Susan Eappen
Sent: Friday, April 5, 2019 2:22 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Lowest energy structure after production MD run

Hello gromacs users,

Since the final structure obtained after production MD run is the average 
structure, how to extract out the lowest energy structure?

Thank you for sharing your knowledge,
Neena
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Re: [gmx-users] Lowest energy structure after production MD run

2019-04-05 Thread Neena Susan Eappen

Hello Simone,

Thank you for detailed reply, I am sorry, I got this incorrect information from 
my search on google. So the final structure is the state at the final time of 
simulation or basically the last frame, great!
I am new to gromacs, my goal is to understand the structure of a peptide in 
vacuum. From my experiments on the millisecond timescale, I see atleast two 
conformations in vacuum (with distinct collisional cross sections). Yes, that's 
exactly what I was looking for an energy landscape of my trajectory, to look 
for atleast two highly populated low energy structures and somehow extract out 
CCS for those. So far I have tried only 1ns MD run, I am trying to get familiar 
with all mdp files before I do a 1µs run.
What did you mean by collective variables?

Thank you for sharing your knowledge,
Neena


From: Neena Susan Eappen
Sent: Friday, April 5, 2019 3:52 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Lowest energy structure after production MD run

Thank you Dr. Dallas,

I am new to gromacs, so I assumed the final structure was average after 
searching on google.

Neena





From: Neena Susan Eappen
Sent: Friday, April 5, 2019 2:22 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Lowest energy structure after production MD run

Hello gromacs users,

Since the final structure obtained after production MD run is the average 
structure, how to extract out the lowest energy structure?

Thank you for sharing your knowledge,
Neena
-- 
Gromacs Users mailing list

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[gmx-users] nstlist changes during equilibration and production

2019-04-15 Thread Neena Susan Eappen

Hello gromacs users,

I set my nstlist to 10 steps for energy minimization, NVT equilibration and MD 
production run. However, for the latter two steps, nstlist changes from 10 to 
100 (My time step for integration was set to 2 fs). Is 20 fs too fast to update 
neighbor list? Any impact on accuracy?

Many thanks,
Neena
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[gmx-users] -ignh command removes protonation site of interest

2019-04-15 Thread Neena Susan Eappen

Hello gromacs users,

I started with a peptide where protonation site was on a carbonyl oxygen. 
However, using -ignh command in pdb2gmx, I lose that proton from there. Any 
insights on how to move forward?

Many thanks,
Neena
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Re: [gmx-users] -ignh command removes protonation site of interest

2019-04-16 Thread Neena Susan Eappen

I am using OPLS-AA force field and there are no parameters for protonated 
carbonyl for alanine residue. How do I go about this?

Thank you,
Neena

From: Neena Susan Eappen
Sent: Monday, April 15, 2019 10:30 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] -ignh command removes protonation site of interest

Hello gromacs users,

I started with a peptide where protonation site was on a carbonyl oxygen. 
However, using -ignh command in pdb2gmx, I lose that proton from there. Any 
insights on how to move forward?

Many thanks,
Neena
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Re: [gmx-users] -ignh command removes protonation site of interest

2019-04-17 Thread Neena Susan Eappen

Hi Justin,

I am trying to simulate a peptide in vacuum and it has been shown that carbonyl 
oxygen is a favorable site of protonation in gas phase, hence I was looking for 
protonated carbonyl force field parameters.

Thank you,
Neena

From: Neena Susan Eappen
Sent: Tuesday, April 16, 2019 7:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] -ignh command removes protonation site of interest

I am using OPLS-AA force field and there are no parameters for protonated 
carbonyl for alanine residue. How do I go about this?

Thank you,
Neena


From: Neena Susan Eappen
Sent: Monday, April 15, 2019 10:30 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] -ignh command removes protonation site of interest

Hello gromacs users,

I started with a peptide where protonation site was on a carbonyl oxygen. 
However, using -ignh command in pdb2gmx, I lose that proton from there. Any 
insights on how to move forward?

Many thanks,
Neena
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[gmx-users] No constraints, default potential?

2019-04-20 Thread Neena Susan Eappen

Hello gromacs users,

When no bond constraints are applied during simulation, what is the default 
potential used to describe bond stretching? Harmonic or Morse?

Many thanks,
Neena
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[gmx-users] Cannot select termini with AMBER99sb-ildn

2019-04-20 Thread Neena Susan Eappen

Hello gromacs users,

I was wondering why with AMBER99sb-ildn force field, peptide termini cannot be 
user defined say like neutral N terminus. Is this because this forcefield is 
mostly for proteins for which N-terminus is always protonated at physiological 
pH?

Many thanks,
Neena
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[gmx-users] Initial velocities before equilibration

2019-04-25 Thread Neena Susan Eappen

Hello gromacs users,

After completing MD production run, I ran a command gmx check for my xtc file. 
However, no velocities were updated in any frame. What could this be due to?

Many thanks,
Neena
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[gmx-users] RMSD command line doubt

2019-04-28 Thread Neena Susan Eappen

Hello gromacs users,

My goal is to calculate all-atom rmsd of every structure in the 
trajectory(.trr) to the final structure after simulation (.gro).

Q1) So, I don't understand the purpose of giving .tpr input file (which was the 
input structure file before production mdrun) as a structure file in the 
command.

gmx rms -f peptide.trr -s peptide.tpr -o rmsd.xvg

Q2) When I use final structure .gro file (after production mdrun), I get the 
following warning:

Masses and atomic (Van der Waals) radii will be guessed based on residue and 
atom names, since they could not be definitively assigned from the information 
in your input files.

Please let me know if I am misunderstanding here anything.

Many thanks,
Neena

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Re: [gmx-users] Average rmsd

2019-04-28 Thread Neena Susan Eappen

Hi Neelam,

I do not have Xmgrace tool, but you can open up the xvg file on excel and 
calculate average.
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[gmx-users] H bond dynamics, remove thermostat?

2019-05-03 Thread Neena Susan Eappen

Hello gromacs users,

I am interested in studying the H-bond dynamics of my protein. Do you recommend 
to turn off thermostat for production run?

Many thanks,
Neena
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[gmx-users] H-Bond from peptide capping group

2019-05-22 Thread Neena Susan Eappen

Hello gromacs users,

I uploaded a peptide structure on VMD with its trajectory (using gromacs 
package) and used H-bond plugin to figure out possible H bonds. The C-terminus 
has a capping amide group. The H-bond plugin never catches any H-bond 
information from that capping group. My guess is the capping group is 
considered as a separate entity (not part of the peptide). Any insight would be 
appreciated.

Thank you,
Neena

P.S. I received no answer to this question on VMD mailing list, hence asking 
here.


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[gmx-users] Segmentation fault, core dumped error

2019-05-24 Thread Neena Susan Eappen

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core 
dumped. Shown below is my gmx version details (if that can point to my 
problem). Any insight would be appreciated.

GROMACS version:2018.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-12 0:35
Built by:   name@HP-PC [CMAKE]
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:   6   Model: 61   Stepping: 4
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags:   march=core-AVX2 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

Thank you,
Neena
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Re: [gmx-users] Segmentation fault, core dumped error

2019-05-28 Thread Neena Susan Eappen

Hello gromacs users,

Is there a reason why segmentation fault appeared when gmx hbond command was 
used?

Thank you,
Neena


From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core 
dumped. Shown below is my gmx version details (if that can point to my 
problem). Any insight would be appreciated.

GROMACS version:2018.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-12 0:35
Built by:   name@HP-PC [CMAKE]<mailto:name@HP-PC%20[CMAKE]>
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:   6   Model: 61   Stepping: 4
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags:   march=core-AVX2 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

Thank you,
Neena
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Re: [gmx-users] Segmentation fault, core dumped error

2019-05-29 Thread Neena Susan Eappen

Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr

Specify 2 groups to analyze:

Group 0 (System) has   130 elements

Group 1 (Protein) has   130 elements

Group 2 (Protein-H) has63 elements

Group 3 (C-alpha) has11 elements

Group 4 (Backbone) has34 elements

Group 5 (MainChain) has47 elements

Group 6 (MainChain+Cb) has58 elements

Group 7 (MainChain+H) has58 elements

Group 8 (SideChain) has72 elements

Group 9 (SideChain-H) has16 elements


Select a group: 1 Selected 1: 'Protein'

Select a group: 1 Selected 1: 'Protein'

Output: Calculating hydrogen bonds in Protein (130 atoms)

Found 13 donors and 25 acceptors

trr version: GMX_trn_file (single precision)

Reading frame   0 time0.000

Will do grid-seach on 2374x2374x2374 grid, rcut=0.35

Segmentation fault (core dumped)

________
From: Neena Susan Eappen
Sent: Tuesday, May 28, 2019 11:31 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

Is there a reason why segmentation fault appeared when gmx hbond command was 
used?

Thank you,
Neena

________
From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core 
dumped. Shown below is my gmx version details (if that can point to my 
problem). Any insight would be appreciated.

GROMACS version:2018.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-12 0:35
Built by:   name@HP-PC [CMAKE]<mailto:name@HP-PC%20[CMAKE]>
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:   6   Model: 61   Stepping: 4
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags:   march=core-AVX2 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

Thank you,
Neena
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Re: [gmx-users] Segmentation fault, core dumped error

2019-05-29 Thread Neena Susan Eappen

Hi Paul Bauer,

I do not have an account on redmine.gromacs.org neither that page allows me to 
create an account. Please let me know what to do.

Hi Najamuddin,

I tried xtc file instead of trr, still same error shows up.

Thank you,
Neena


From: Neena Susan Eappen
Sent: Wednesday, May 29, 2019 5:25 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Segmentation fault, core dumped error


Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr

Specify 2 groups to analyze:

Group 0 (System) has   130 elements

Group 1 (Protein) has   130 elements

Group 2 (Protein-H) has63 elements

Group 3 (C-alpha) has11 elements

Group 4 (Backbone) has34 elements

Group 5 (MainChain) has47 elements

Group 6 (MainChain+Cb) has58 elements

Group 7 (MainChain+H) has58 elements

Group 8 (SideChain) has72 elements

Group 9 (SideChain-H) has16 elements


Select a group: 1 Selected 1: 'Protein'

Select a group: 1 Selected 1: 'Protein'

Output: Calculating hydrogen bonds in Protein (130 atoms)

Found 13 donors and 25 acceptors

trr version: GMX_trn_file (single precision)

Reading frame   0 time0.000

Will do grid-seach on 2374x2374x2374 grid, rcut=0.35

Segmentation fault (core dumped)

________
From: Neena Susan Eappen
Sent: Tuesday, May 28, 2019 11:31 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

Is there a reason why segmentation fault appeared when gmx hbond command was 
used?

Thank you,
Neena

________
From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core 
dumped. Shown below is my gmx version details (if that can point to my 
problem). Any insight would be appreciated.

GROMACS version:2018.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-12 0:35
Built by:   name@HP-PC [CMAKE]<mailto:name@HP-PC%20[CMAKE]>
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:   6   Model: 61   Stepping: 4
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags:   march=core-AVX2 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

Thank you,
Neena
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[gmx-users] Coordinates of structures from a .trr file

2019-06-01 Thread Neena Susan Eappen

Hello gromacs users,

How to extract coordinates (and thereby make a PDB file) for say structure at 
time 200 ps from a 1 ns production run?

Thank you,
Neena
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[gmx-users] List of H-bond donors and acceptors

2019-06-02 Thread Neena Susan Eappen

Hello gromacs users,

gmx hbond only gives me number of Hbonds as a function of trajectory time, is 
there a way to get a specific list of donors and acceptors as a function of 
time?

Thank you,
Neena
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[gmx-users] OPLS-ff topology file for modified residue procedure?

2019-06-18 Thread Neena Susan Eappen

Hello gromacs users,

For MD simulations of a peptide in vacuum, I want to find OPLS force field 
compatible parameters for modified alanine residue in the peptide (with the 
carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a 
protonation site is possible in gas phase.

I was wondering do I use the mktop program suggested by gromacs to generate it?

Thank you,
Neena
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Re: [gmx-users] OPLS-ff topology file for modified residue procedure?

2019-06-19 Thread Neena Susan Eappen

Hello gromacs users,

For MD simulations of a peptide in vacuum, I want to find OPLS force field 
compatible parameters for modified alanine residue in the peptide (with the 
carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a 
protonation site is possible in gas phase.

I was wondering do I use the mktop program suggested by gromacs to generate 
dihedrals, partial charges? Or use DFT for parameterization?

Thank you,
Neena

From: Neena Susan Eappen
Sent: Tuesday, June 18, 2019 11:35 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] OPLS-ff topology file for modified residue procedure?

Hello gromacs users,

For MD simulations of a peptide in vacuum, I want to find OPLS force field 
compatible parameters for modified alanine residue in the peptide (with the 
carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a 
protonation site is possible in gas phase.

I was wondering do I use the mktop program suggested by gromacs to generate it?

Thank you,
Neena
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[gmx-users] Difference between equilibration and production run

2019-06-24 Thread Neena Susan Eappen

Hello gromacs users,

I used NVT ensemble at constant temperature during both 
equilibration and data collection step. I observed that my peptide turned from 
extended coil to helical form only in the data collection step (very early on 
in the trajectory). Yes, a helical structure is theoretically expected for my 
peptide.

However, I do not understand why I did not see this during equilibration. The 
observation is similar regardless of equilibration time.

Any insight would be appreciated,
Thank you,
Neena
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[gmx-users] Generate OPLS Parameters for a modified residue

2019-06-25 Thread Neena Susan Eappen

Hello gromacs users,

Any suggestions on how to generate OPLS ff parameters for a modified residue? I 
found a few servers (listed below):

- TPPmktop: http://erg.biophys.msu.ru/tpp/
- LigParGen: http://zarbi.chem.yale.edu/ligpargen/

Can I get your insights if you have used anyone of these tools?

Many thanks,
Neena





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[gmx-users] Repeat Simulation n times

2019-07-08 Thread Neena Susan Eappen

Hello gromacs users,

To repeat a simulation say 50 times, do I manually start from minimization step 
to data collection 50 times, or is there anything I can write in the command 
line?

Thank you,
Neena
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[gmx-users] OPLS parameterization for a modified aminoacid

2019-07-31 Thread Neena Susan Eappen

Hello gromacs users,

Do I use this reference for the procedure to find OPLS parameters for a 
modified aminoacid?

Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: Evaluation 
and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison 
with Accurate Quantum Chemical Calculations on Peptides †. J. Phys. Chem. B. 
105, 6474–6487 (2001).

Many thanks,
Neena
Graduate Student
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Re: [gmx-users] OPLS parameterization for a modified aminoacid

2019-08-01 Thread Neena Susan Eappen

Hello gromacs users,

I want to thoroughly learn how OPLS parameters were found for modified 
aminoacids (for instance aspartic acid versus neutral aspartic acid). I am 
currently having unluck using DFT for parameterization.

Any help appreciated,
Neena

From: Neena Susan Eappen
Sent: Wednesday, July 31, 2019 11:54 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] OPLS parameterization for a modified aminoacid

Hello gromacs users,

Do I use this reference for the procedure to find OPLS parameters for a 
modified aminoacid?

Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: Evaluation 
and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison 
with Accurate Quantum Chemical Calculations on Peptides †. J. Phys. Chem. B. 
105, 6474–6487 (2001).

Many thanks,
Neena
Graduate Student
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[gmx-users] SIMD: SSE2 or AVX2_256?

2019-08-06 Thread Neena Susan Eappen

Hello gromacs users,

I got the following message when I was running grompp command:

-Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see 
log).
The current CPU can measure timings more accurately than the code in gmx mdrun 
was configured to use. This might affect your simulation speed as accurate 
timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake 
option.---

I was wondering is this a necessity?

Thank you,
Neena
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[gmx-users] Relation between tau_t and nstxout

2019-08-08 Thread Neena Susan Eappen

Hello gromacs users,

I am using Nose-hoover thermostat, is it correct to say that tau_t has to be 
less than or equal to nstxout/ nstvout? Because I do not want to record 
position and velocity before the temperature has been relaxed to target 
temperature?
Please correct me.

Thank you,
Neena
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[gmx-users] Change forcefield directory

2019-08-08 Thread Neena Susan Eappen

Hello gromacs users,

I had to add a new residue into forcefield, that required copying aminoacid.rtp 
file into my home folder (as gromacs is installed on a shared network).
During pdb2gmx, how can I redirect the following to my home folder? Where can I 
edit this change in forcefield directory?

Select the Force Field:
>From '/programs/x86_64-linux/gromacs/2018.4/share/gromacs/top':

Many thanks,
Neena
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[gmx-users] Residue XXX not found in residue topology database

2019-08-26 Thread Neena Susan Eappen

Hello gromacs users,

I saw the following error for a modified residue I added though I edited all 
necessary files including PDB. I also read the gromacs documentation on this 
error.

Residue XXX not found in residue topology database.

Any hints on what might be happening?

Many thanks,
Neena
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[gmx-users] Simulated Annealing Procedure

2019-09-19 Thread Neena Susan Eappen

Hello gromacs users,

My goal is to do a better conformational sampling of my peptides in vacuum. I 
was wondering do I simulated annealing with position restraints or not?

Many thanks,
Neena

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[gmx-users] Neena Susan Eappen shared "C_Terminus" with you.

2019-09-23 Thread Neena Susan Eappen

Here's the document that Neena Susan Eappen shared with you.
[cid:ffd92ec7-9102-4ae4-ae1b-93cc4e9badaa]  This link only works for the 
direct recipients of this message.
[cid:2916f182-2b48-4170-843a-77c609e1ae08] 
<https://utoronto-my.sharepoint.com:443/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWi2E2SPPMRGg75A6kO4uNsBKmWuMk9yFIuTyl9C38DdIA?e=4%3agpaF4w&at=9>
  
<https://utoronto-my.sharepoint.com:443/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWi2E2SPPMRGg75A6kO4uNsBKmWuMk9yFIuTyl9C38DdIA?e=4%3agpaF4w&at=9>
C_Terminus

Open 
<https://utoronto-my.sharepoint.com:443/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWi2E2SPPMRGg75A6kO4uNsBKmWuMk9yFIuTyl9C38DdIA?e=4%3agpaF4w&at=9>

[Microsoft] [Microsoft]
Sender will be notified when you open this link for the first time.
Microsoft respects your privacy. To learn more, please read our Privacy 
Statement.<https://canadaeastr-notifyp.svc.ms:443/api/v2/tracking/method/Click?mi=ZFm-hehyzUObs7dSV17CqQ&ru=https%3a%2f%2fprivacy.microsoft.com%2fprivacystatement&tc=PrivacyStatement&cs=0314d9fa12424d266f2bced0d585848e>
Microsoft Corporation, One Microsoft Way, Redmond, WA 98052

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[gmx-users] Problem with adding New peptide Terminus

2019-09-23 Thread Neena Susan Eappen

Hello gromacs users,

I was trying to add a modified C-terminus for my peptide, an amide group at the 
C-terminus with a protonated carbonyl oxygen,  formula here 
[https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] 
C_Terminus.png

I edited the tdb in the following way

[ protonatedamide ]
[ replace ]
C CT5 opls_968 12.011   0.641
O O1  opls_967 15.9994 -0.188
[ add ]
1 1 NT CT5 O1   CA
 opls_237 14.0067   -0.76
2 3 HT NT CT5 CA
  opls_240 1.008   0.38
1 2 HO1 O1 CT5 CA
  opls_966 1.008   0.547
[ bonds ]
HO1O1
NT   CT5
HT   N

I got an error message saying C atom in the input file does not correspond to 
topology database.
I do not understand why I got this error message.
Please let me know where I am going wrong.

Thank you,
Neena
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Re: [gmx-users] Problem with adding New peptide Terminus

2019-09-26 Thread Neena Susan Eappen

Hi Justin,

This is the actual error message,

Residue 3 named ALA of a molecule in the input file was mapped to an entry in 
the topology database, but the atom C used in that entry is not found in the 
input file. Perhaps your atom and/or residue naming needs to be fixed.

I was trying to add a modified C-terminus for my peptide, an amide group at the 
C-terminus with a protonated carbonyl oxygen,  formula here 
[https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] 
C_Terminus.png<https://utoronto-my.sharepoint.com/personal/neena_susaneappen_mail_utoronto_ca/_layouts/15/onedrive.aspx?id=%2Fpersonal%2Fneena%5Fsusaneappen%5Fmail%5Futoronto%5Fca%2FDocuments%2FC%5FTerminus%2Epng&parent=%2Fpersonal%2Fneena%5Fsusaneappen%5Fmail%5Futoronto%5Fca%2FDocuments&originalPath=aHR0cHM6Ly91dG9yb250by1teS5zaGFyZXBvaW50LmNvbS86aTovZy9wZXJzb25hbC9uZWVuYV9zdXNhbmVhcHBlbl9tYWlsX3V0b3JvbnRvX2NhL0VXdEFoTWRqWHF4Q2hHUlpYV083eWpBQkh0eVdVdy1LQUxtanpINWlIR3BFY0E_cnRpbWU9clF6QkZveEMxMGc>

This is the content of my PDB file
[https://r1.res.outlook.com/owa/prem/images/txt_16x16.png]PDBcontent.txt<https://utoronto-my.sharepoint.com/:t:/g/personal/neena_susaneappen_mail_utoronto_ca/EaBgTX45S9ZCv3Kn0br_-eoBdMP5dP_mGFQWVBKy9qofuw?email=gromacs.org_gmx-users%40maillist.sys.kth.se&e=r0P5af>

I edited the tdb.c in the following way (no change in the aminoacid.rtp file)

[ protonatedamide ]
[ replace ]
C CT5 opls_968 12.011   0.641
O O1  opls_967 15.9994 -0.188
[ add ]
1 1 NT CT5 O1   CA
 opls_237 14.0067   -0.76
2 3 HT NT CT5 CA
 opls_240  1.008   0.38
1 2 HO1 O1 CT5 CA
  opls_966 1.008   0.547
[ bonds ]
HO1O1
NT   CT5
HT   N

Thank you for your time,
Neena


________
From: Neena Susan Eappen
Sent: Tuesday, September 24, 2019 1:48 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Problem with adding New peptide Terminus

Hello gromacs users,

I was trying to add a modified C-terminus for my peptide, an amide group at the 
C-terminus with a protonated carbonyl oxygen,  formula here 
[https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] 
C_Terminus.png<https://utoronto-my.sharepoint.com/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWtAhMdjXqxChGRZXWO7yjABHtyWUw-KALmjzH5iHGpEcA>

I edited the tdb in the following way

[ protonatedamide ]
[ replace ]
C CT5 opls_968 12.011   0.641
O O1  opls_967 15.9994 -0.188
[ add ]
1 1 NT CT5 O1   CA
 opls_237 14.0067   -0.76
2 3 HT NT CT5 CA
  opls_240 1.008   0.38
1 2 HO1 O1 CT5 CA
  opls_966 1.008   0.547
[ bonds ]
HO1O1
NT   CT5
HT   N

I got an error message saying C atom in the input file does not correspond to 
topology database.
I do not understand why I got this error message.
Please let me know where I am going wrong.

Thank you,
Neena
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[gmx-users] Simulated Annealing General Procedure

2019-10-29 Thread Neena Susan Eappen

Hello gromacs users,

My goal is to do a better conformational sampling of my peptides using 
simulated annealing. Is my following procedure correct?

1- Energy minimization
2- NVT equilibration with position restraints say at 600 K for 100 ps
3- Simulated annealing with position restraints to cool down from 600 K to 300 
K for 152 ps, with no velocity generation
4- Production simulation at 300 K for 10 ns without position restraints, with 
no velocity generation
5- Another step of energy minimization
6- Then repeat steps 2-6 multiple times with initially minimized structure from 
step 1

Many thanks,
Neena
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Re: [gmx-users] What is the "gen-vel" used for?

2020-01-03 Thread Neena Susan Eappen

Yeping Sun,

Quoting Justin's answer for a similar question I had on how to repeat a 
simulation say 10 times
 " To run 10 independent simulations, I would run minimization once and start 
from 10 new equilibration runs, each with a different set of initial velocities 
(change gen_seed or simply set to -1).That approach may not be as robust as 
starting from 10 different configurations, but the exact approach depends on 
the system in question".




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Re: [gmx-users] amide-capped C-terminus; OPLS force field

2020-01-03 Thread Neena Susan Eappen

I do this by adding amide group at the C-terminus on Pymol, use -ter flag 
during gmx pdb2gmx command, select None (for C-terminus), N and H in that amide 
group are automatically recognized as atom types opls 237 and opls 240 
respectively. The net charge of system remains neutral.
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[gmx-users] Simulated Annealing command line

2020-01-05 Thread Neena Susan Eappen

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, 
production run, energy minimization) say n times with the energy minimized 
structure from end of cycle 1 to be used as starting structure for cycle 2. I 
was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab, U of T
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Re: [gmx-users] Simulated Annealing command line

2020-01-07 Thread Neena Susan Eappen

Hi Kenny,

Thank you for your answer, but I did not understand clearly. For say 30 cycles 
of simulated annealing, what I have been doing currently is going through the 
following steps ( equilibration, annealing, production run, energy 
minimization) 30 times by changing names of input and output files every cycle.
My question is say after the 1st cycle, is there a way to input a single 
command line to repeat this process say the remaining 29 times by using energy 
minimized structure from the end of every cycle as the starting structure for 
the next cycle.

Any insight would be appreciated,

Thank you,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, 
production run, energy minimization) say n times with the energy minimized 
structure from end of cycle 1 to be used as starting structure for cycle 2. I 
was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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Re: [gmx-users] Simulated Annealing command line

2020-01-07 Thread Neena Susan Eappen

Hi Justin,

Thank you for your answer. I haven't written scripts before, so I was wondering 
is there a sample script I can see for looping in gromacs.

Thanks,
Neena

From: Neena Susan Eappen 
Sent: Tuesday, January 7, 2020 1:57 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] Simulated Annealing command line

Hi Kenny,

Thank you for your answer, but I did not understand clearly. For say 30 cycles 
of simulated annealing, what I have been doing currently is going through the 
following steps ( equilibration, annealing, production run, energy 
minimization) 30 times by changing names of input and output files every cycle.
My question is say after the 1st cycle, is there a way to input a single 
command line to repeat this process say the remaining 29 times by using energy 
minimized structure from the end of every cycle as the starting structure for 
the next cycle.

Any insight would be appreciated,

Thank you,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Simulated Annealing command line

Hello gromacs users,

For simulated annealing, I want to repeat cycle (equilibration, annealing, 
production run, energy minimization) say n times with the energy minimized 
structure from end of cycle 1 to be used as starting structure for cycle 2. I 
was wondering is there a way to do this as a loop with just one command line?

Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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[gmx-users] Script for looping n simulations

2020-02-15 Thread Neena Susan Eappen

Hello gromacs users,

I was wondering how to write a script to repeat a simulation (equilibration and 
production) n times, with each cycle starting with structure from the end of 
previous cycle.

Many thanks,
Neena
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Re: [gmx-users] Script for looping n simulations

2020-02-22 Thread Neena Susan Eappen

Thank you Justin, just sharing the sample script here:

#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
--
Question: Now that I have n .edr files, is there a script I can write to 
extract say potential energy from these n files?

Thank you for your time and knowledge,
Neena



From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Script for looping n simulations

Hello gromacs users,

I was wondering how to write a script to repeat a simulation (equilibration and 
production) n times, with each cycle starting with structure from the end of 
previous cycle.

Many thanks,
Neena
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Re: [gmx-users] Script for looping n simulations

2020-02-22 Thread Neena Susan Eappen

Thank you Miro, but I don't think I found what I wanted in your script. Let me 
be more clear: I ran n simulations in a loop, I have corresponding n energy 
files (.edr). I want to extract potential energy from each file. How would I go 
about that with a script?

Many thanks,
Neena

From: Neena Susan Eappen 
Sent: Saturday, February 22, 2020 2:41 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] Script for looping n simulations

Thank you Justin, just sharing the sample script here:

#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
--
Question: Now that I have n .edr files, is there a script I can write to 
extract say potential energy from these n files?

Thank you for your time and knowledge,
Neena



From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Script for looping n simulations

Hello gromacs users,

I was wondering how to write a script to repeat a simulation (equilibration and 
production) n times, with each cycle starting with structure from the end of 
previous cycle.

Many thanks,
Neena
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Re: [gmx-users] Script for looping n simulations

2020-03-10 Thread Neena Susan Eappen

Hi Justin,

I tried that script out, but I want the output in a different way. So I have n 
log files (.log), and I want to extract potential energy value say from line x 
from all n log files. Is there a way I can export all these potential energy 
values into one text file with one script?

Many thanks,
Neena

From: Neena Susan Eappen 
Sent: Saturday, February 22, 2020 4:28 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] Script for looping n simulations

Thank you Miro, but I don't think I found what I wanted in your script. Let me 
be more clear: I ran n simulations in a loop, I have corresponding n energy 
files (.edr). I want to extract potential energy from each file. How would I go 
about that with a script?

Many thanks,
Neena

From: Neena Susan Eappen 
Sent: Saturday, February 22, 2020 2:41 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] Script for looping n simulations

Thank you Justin, just sharing the sample script here:

#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
--
Question: Now that I have n .edr files, is there a script I can write to 
extract say potential energy from these n files?

Thank you for your time and knowledge,
Neena



From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Script for looping n simulations

Hello gromacs users,

I was wondering how to write a script to repeat a simulation (equilibration and 
production) n times, with each cycle starting with structure from the end of 
previous cycle.

Many thanks,
Neena
-- 
Gromacs Users mailing list

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

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Re: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx

2020-03-14 Thread Neena Susan Eappen

Hi Billy,

  1.  Firstly, why is that gromacs reads MYR as residue 2 and not 1? What does 
it say in your PDB file?
  2.  There is no atom labelled C in your MYR atom list. Looks like you have 
listed atom C in the dihedral type (ffnonbonded.itp), change that.
  3.  If you think it is not recognizing the link between MYR and B3K, then in 
the aminoacids.rtp file, for B3K, check if in the improper dihedral (involving 
terminal N) if there is atom C listed instead of C1. If yes, change it to C1.

Hope this helps,
Neena
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[gmx-users] No default bond types

2020-03-24 Thread Neena Susan Eappen

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

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Re: [gmx-users] No default bond types

2020-03-25 Thread Neena Susan Eappen

Hi Alessandra,

For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp 
file. However, the command grompp gave error for one bond and 6 angle types 
although I have all in there. Is there a way to resolve this?

From: Neena Susan Eappen
Sent: Wednesday, March 25, 2020 3:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] No default bond types

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

-- 
Gromacs Users mailing list

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

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Re: [gmx-users] No default bond types

2020-03-25 Thread Neena Susan Eappen

Hi Justin,

Yes errors from grompp are very clear. Initially, I had errors for all four 4 
new bond and 9 new angle types, grompp specifically stated which line in the 
topology file was missing. Accordingly, I added parameters for all in the 
ffbonded.itp file correctly. Even after that, I still wonder why I have 
errors



From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 8:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Alessandra,

For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp 
file. However, the command grompp gave error for one bond and 6 angle types 
although I have all in there. Is there a way to resolve this?

From: Neena Susan Eappen
Sent: Wednesday, March 25, 2020 3:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] No default bond types

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

-- 
Gromacs Users mailing list

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

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Re: [gmx-users] No default bond types

2020-03-25 Thread Neena Susan Eappen

I am sorry that I previously did not attach any files as I was confident how I 
edited. Problem Solved: By just adding those missing parameters in the topology 
file itself. I am showing values below for future reference:

On grompp, following error came up:

ERROR 1 [file topol.top, line 84]:
  No default bond types

 Line 84 in topol.top :  1420 1

Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified 
alanine residue, for which I already had parameters in the ffbonded.itp file 
under [ bond types] as shown below:

CAC15 10.14900   334720.0

Problem solved by changing that line 84 in topology file

  Line 84: 1420 10.14900   334720.0


From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 11:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Justin,

Yes errors from grompp are very clear. Initially, I had errors for all four 4 
new bond and 9 new angle types, grompp specifically stated which line in the 
topology file was missing. Accordingly, I added parameters for all in the 
ffbonded.itp file correctly. Even after that, I still wonder why I have 
errors



From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 8:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Alessandra,

For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp 
file. However, the command grompp gave error for one bond and 6 angle types 
although I have all in there. Is there a way to resolve this?

From: Neena Susan Eappen
Sent: Wednesday, March 25, 2020 3:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] No default bond types

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

-- 
Gromacs Users mailing list

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

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

Re: [gmx-users] No default bond types

2020-03-25 Thread Neena Susan Eappen

Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH 
(modified alanine)

 opls_968   12.01100  ; C15 in ALH

From: Neena Susan Eappen 
Sent: Thursday, March 26, 2020 12:47 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

I am sorry that I previously did not attach any files as I was confident how I 
edited. Problem Solved: By just adding those missing parameters in the topology 
file itself. I am showing values below for future reference:

On grompp, following error came up:

ERROR 1 [file topol.top, line 84]:
  No default bond types

 Line 84 in topol.top :  1420 1

Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified 
alanine residue, for which I already had parameters in the ffbonded.itp file 
under [ bond types] as shown below:

CAC15 10.14900   334720.0

Problem solved by changing that line 84 in topology file

  Line 84: 1420 10.14900   334720.0

From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 11:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Justin,

Yes errors from grompp are very clear. Initially, I had errors for all four 4 
new bond and 9 new angle types, grompp specifically stated which line in the 
topology file was missing. Accordingly, I added parameters for all in the 
ffbonded.itp file correctly. Even after that, I still wonder why I have 
errors

From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 8:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Alessandra,

For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp 
file. However, the command grompp gave error for one bond and 6 angle types 
although I have all in there. Is there a way to resolve this?

From: Neena Susan Eappen
Sent: Wednesday, March 25, 2020 3:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] No default bond types

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

-- 
Gromacs Users mailing list

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

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

Re: [gmx-users] No default bond types

2020-03-25 Thread Neena Susan Eappen

Interesting, I did have that line in ffnonbonded.itp

opls_968   C15  6  12.01100 0.641   A3.55000e-01  3.17984e-01

From: Neena Susan Eappen 
Sent: Thursday, March 26, 2020 1:04 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH 
(modified alanine)

 opls_968   12.01100  ; C15 in ALH

From: Neena Susan Eappen 
Sent: Thursday, March 26, 2020 12:47 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

I am sorry that I previously did not attach any files as I was confident how I 
edited. Problem Solved: By just adding those missing parameters in the topology 
file itself. I am showing values below for future reference:

On grompp, following error came up:

ERROR 1 [file topol.top, line 84]:
  No default bond types

 Line 84 in topol.top :  1420 1

Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified 
alanine residue, for which I already had parameters in the ffbonded.itp file 
under [ bond types] as shown below:

CAC15 10.14900   334720.0

Problem solved by changing that line 84 in topology file

  Line 84: 1420 10.14900   334720.0

From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 11:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Justin,

Yes errors from grompp are very clear. Initially, I had errors for all four 4 
new bond and 9 new angle types, grompp specifically stated which line in the 
topology file was missing. Accordingly, I added parameters for all in the 
ffbonded.itp file correctly. Even after that, I still wonder why I have 
errors

From: Neena Susan Eappen 
Sent: Wednesday, March 25, 2020 8:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] No default bond types

Hi Alessandra,

For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp 
file. However, the command grompp gave error for one bond and 6 angle types 
although I have all in there. Is there a way to resolve this?

From: Neena Susan Eappen
Sent: Wednesday, March 25, 2020 3:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] No default bond types

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

-- 
Gromacs Users mailing list

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

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

[gmx-users] Effect of atomic charge on bonding parameters

2020-03-31 Thread Neena Susan Eappen

Hello gromacs users,

Following two atoms (opls_ 237 and 238) have different atomic charges, but same 
bond type and thereby same parameters in the ffbonded.itp file. Is the effect 
of charge on bonding ignored? Is that possible?

; name   bond_type masscharge   ptype  sigma  
epsilon
opls_237 N714.00670 -0.760   A  3.25000e-01  
7.11280e-01
opls_238 N714.00670 -0.500   A  3.25000e-01  
7.11280e-01

(Taken from ffnonbonded.itp file)

Thank you,
Neena
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Re: [gmx-users] Effect of atomic charge on bonding parameters

2020-04-02 Thread Neena Susan Eappen

Hi Justin,

What is the criteria for opls bond types?

Thank you,
Neena

From: Neena Susan Eappen
Sent: Wednesday, April 1, 2020 12:05 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Effect of atomic charge on bonding parameters

Hello gromacs users,

Following two atoms (opls_ 237 and 238) have different atomic charges, but same 
bond type and thereby same parameters in the ffbonded.itp file. Is the effect 
of charge on bonding ignored? Is that possible?

; name   bond_type masscharge   ptype  sigma  
epsilon
opls_237 N714.00670 -0.760   A  3.25000e-01  
7.11280e-01
opls_238 N714.00670 -0.500   A  3.25000e-01  
7.11280e-01

(Taken from ffnonbonded.itp file)

Thank you,
Neena
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Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs

2020-04-12 Thread Neena Susan Eappen

Hi Lazaro,

Please upload your minim.mdp file and potential plot say on your google drive/ 
one drive/ dropbox. Make it shareable and provide the link to it here. I do 
vacuum simulations, so I can guide you.

Neena

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se 

Sent: Sunday, April 12, 2020 3:25 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36

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Today's Topics:

   1. Re: duplicate angle index- angle restraint (Sadaf Rani)
   2. Re: duplicate angle index- angle restraint (Justin Lemkul)
   3. Electric field (Prithwish Nandi)
   4. Re: Electric field (Prithwish Nandi)
   5. how to run a MD of a small molecule in vacuum in Gromacs
  (Lazaro Castanedo)

--

Message: 1
Date: Sun, 12 Apr 2020 12:40:35 +0100
From: Sadaf Rani 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear Justin
 As per table 5.14 in manual, For angle restraints it selects

[image: image.png]
Also in manual under heading *Angle restraints*, it is mentioned that these
are used to restrain the angle between two pairs of particles or between
one pair of particles and the ?-axis.
Could you please correct me in setting this?

Thanks.
Sadaf

--

Message: 2
Date: Sun, 12 Apr 2020 07:44:57 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 4/12/20 7:40 AM, Sadaf Rani wrote:
> Dear Justin
>   As per table 5.14 in manual, For angle restraints it selects
>
> [image: image.png]
> Also in manual under heading *Angle restraints*, it is mentioned that these
> are used to restrain the angle between two pairs of particles or between
> one pair of particles and the ?-axis.
> Could you please correct me in setting this?

I've never used angle restraints, but clearly grompp is not expecting 4
atoms, as its error message clearly states. It is expecting to read 3
atoms, like a conventional angle.

Either there is a bug in the code or a bad description in the manual;
you'll need to look into which that is and please submit a bug report
via https://gitlab.com/gromacs

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--

Message: 3
Date: Sun, 12 Apr 2020 14:15:11 +0100
From: Prithwish Nandi 
To: gmx-us...@gromacs.org
Subject: [gmx-users] Electric field
Message-ID: <46810bf1-efc3-4e89-82c3-cb22198d3...@ichec.ie>
Content-Type: text/plain;   charset=us-ascii

Hi,
I am trying to generate an alternating e-field using gromcas input as following:

electric-field-x = 1.5 1  0  0

E0= 2 V/nm, omega = 1 cycle/ps

This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second.

I ran this input with mdrun -field option for a sanity check.

I plotted field.xvg .

Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period.
It is only 1/4 cycle of a cosine wave.

So, can you please point out what is that I am missing here?

Thanks,

PKN\\

--

Message: 4
Date: Sun, 12 Apr 2020 14:48:20 +0100
From: Prithwish Nandi 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Electric field
Message-ID: <61883bae-5dac-46b1-ad2d-64ee5ec34...@ichec.ie>
Content-Type: text/plain;   charset=us-ascii

Please ignore my message.
I figured it out.
It should be  2*pi*1 = 6.28 for omega to generate a full cycle.

> On 12 Apr 2020, at 14:15, Prithwish Nandi  wrote:
>
> Hi,
> I am trying to generate an alternating e-field using gromcas input as 
> following:
>
> electric-field-x = 1.5 1  0  0
>
> E0= 2 V/nm, omega = 1 cycle/ps
>
> This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second.
>
> I ran this input with mdrun -field

Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs

2020-04-12 Thread Neena Susan Eappen

Try the below minim.mdp parameters which has worked well for vacuum 
simulations. Proper way to do vacuum simulations: no PBC, PME and cutoffs. To 
reduce computation time, Konermann Lab solved it by implementing pseudo-PBC 
conditions. Their paper explains it very clearly (link here): 
https://www.ncbi.nlm.nih.gov/pubmed/29678588

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steep descent energy 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Minimization step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform
nstxout = 100   ; Number of steps to elapse between writing 
coordinates to output trajectory file

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 10; Frequency to update the neighbor list and long 
range forces
cutoff-scheme   = Verlet; Buffered neighbor searching
ns_type = grid  ; Method to determine neighbor list (simple, grid)
coulombtype = cutoff; Treatment of long range electrostatic interactions
rcoulomb= 333.3 ; Short-range electrostatic cut-off
vdwtype = cutoff; Treatment of long range Van der Waals interactions
rvdw= 333.3 ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions in all 3 dimensions
rlist   = 333.3 ; short-range neighbour list cut-off



From: Neena Susan Eappen 
Sent: Sunday, April 12, 2020 4:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: Re: [gmx-users] how to run a MD of a small molecule in vacuum in 
Gromacs

Hi Lazaro,

Please upload your minim.mdp file and potential plot say on your google drive/ 
one drive/ dropbox. Make it shareable and provide the link to it here. I do 
vacuum simulations, so I can guide you.

Neena


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se 

Sent: Sunday, April 12, 2020 3:25 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36

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Today's Topics:

   1. Re: duplicate angle index- angle restraint (Sadaf Rani)
   2. Re: duplicate angle index- angle restraint (Justin Lemkul)
   3. Electric field (Prithwish Nandi)
   4. Re: Electric field (Prithwish Nandi)
   5. how to run a MD of a small molecule in vacuum in Gromacs
  (Lazaro Castanedo)


--

Message: 1
Date: Sun, 12 Apr 2020 12:40:35 +0100
From: Sadaf Rani 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear Justin
 As per table 5.14 in manual, For angle restraints it selects

[image: image.png]
Also in manual under heading *Angle restraints*, it is mentioned that these
are used to restrain the angle between two pairs of particles or between
one pair of particles and the ?-axis.
Could you please correct me in setting this?

Thanks.
Sadaf

--

Message: 2
Date: Sun, 12 Apr 2020 07:44:57 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 4/12/20 7:40 AM, Sadaf Rani wrote:
> Dear Justin
>   As per table 5.14 in manual, For angle restraints it selects
>
> [image: image.png]
> Also in manual under heading *Angle restraints*, it is mentioned that these
> are used to restrain the angle between two pairs of particles or between
> one pair of particles and the ?-axis.
> Could you please correct me in setting this?

I've never used angle restraints, but clearly grompp is not expecting 4
atoms, as its error message clearly states. It is expecting to read 3
atoms, like a conventional angle.

Either there is a bug in the code or a bad description in the manual;
you'll need to look into which

[gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

2020-04-27 Thread Neena Susan Eappen

Hello gromacs users,

My peptide has an amide group at the C-terminus. Hydrogen bond analysis using 
gmx hbond does not take into account H-bond donors (NH2) from the amide group 
(Note: this NH2 is considered as a residue according to opls ff). What might be 
happening here?

Many thanks,
Neena
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Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

2020-05-05 Thread Neena Susan Eappen

Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H 
as donor when part of NH2 group. Please take a look at this file.
https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing

Many thanks,
Neena


From: Neena Susan Eappen
Sent: Tuesday, April 28, 2020 1:50 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis

Hello gromacs users,

My peptide has an amide group at the C-terminus. Hydrogen bond analysis using 
gmx hbond does not take into account H-bond donors (NH2) from the amide group 
(Note: this NH2 is considered as a residue according to opls ff). What might be 
happening here?

Many thanks,
Neena
-- 
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
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mail to gmx-users-requ...@gromacs.org.

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