Re: [gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

On 1/20/16 3:48 AM, Dries Van Rompaey wrote:

Hi Justin and Marco,

Thanks for your reply. I get this behaviour when I specify the default NH3+
and COO- termini through -ter, as well as when I don't use the -ter flag.
Selecting the COOH terminus type removed the warning for the C-terminus,
but selecting the NH2 terminus type did't remove the warning for the
N-terminus. That's not a very physiological state, however.

Can anyone replicate this error?



I can't trigger the same with 5.1 or with current git master.  Try from a fresh 
install and make sure no one has messed with your force field files.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Error estimate for order parameter

[Justin Lemkul]

On 1/20/16 1:31 PM, m g wrote:

Dear all,How can i calculate the error bar for order parameter in gromacs? 
which command must be use?



As you would any other error bar, by running the analysis over replicate 
simulations or in blocks of time with -b and -e.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] find hbond between different groups during simulation

[Justin Lemkul]

On 1/20/16 4:08 AM, Mahboobe Sadr wrote:

Dear all,

I want to find hydrogen bonds between waters and The protein. since in each
frame I selected some specifc waters, I want to find hydrogen bonds during
simulation for different waters(which are in the pore of the protein) and
the protein.
  as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
couldn't find the hbond i want.



Use gmx select to get per-frame index groups that satisfy the selection 
criteria, then run the analysis frame by frame.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Constraints errors

[Alireza Moradzadeh]

Dear Users,
I want to simulate [BMIM][PF6] using following itp
[ moleculetype ]
PF6 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 P 1 PF6 P1 1 1.13 30.974
2 FP 1 PF6 F2 2 -0.33 18.998
3 FP 1 PF6 F3 3 -0.33 18.998
4 FP 1 PF6 F4 4 -0.33 18.998
5 FP 1 PF6 F5 5 -0.33 18.998
6 FP 1 PF6 F6 6 -0.33 18.998
7 FP 1 PF6 F7 7 -0.33 18.998
[ bonds ]
1 2 1
1 3 1
1 4 1
1 5 1
1 6 1
1 7 1
[ angles ]
2 1 3 1
2 1 4 1
2 1 6 1
2 1 7 1
3 1 4 1
3 1 5 1
3 1 7 1
4 1 5 1
4 1 6 1
5 1 6 1
5 1 7 1
6 1 7 1
2 1 5 1 180. 1165.
3 1 6 1 180. 1165.
4 1 7 1 180. 1165.

But I get following errors for both of my molecules.

Molecule type "PF" has 21 constraints.
For stability and efficiency reasons there should not be more constraints
more than internal degree of freedoms: 15
Is it right to use maxwarn in this case?!


Best Regards,
Alireza Moradzadeh
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Re: [gmx-users] find hbond between different groups during simulation

[Mahboobe Sadr]

  Does it mean,  i can't do that automatically??



On Thursday, January 21, 2016, Justin Lemkul  wrote:
>
>
> On 1/20/16 4:08 AM, Mahboobe Sadr wrote:
>>
>> Dear all,
>>
>> I want to find hydrogen bonds between waters and The protein. since in
each
>> frame I selected some specifc waters, I want to find hydrogen bonds
during
>> simulation for different waters(which are in the pore of the protein) and
>> the protein.
>>   as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
>> couldn't find the hbond i want.
>>
>
> Use gmx select to get per-frame index groups that satisfy the selection
criteria, then run the analysis frame by frame.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] Relative alchemical free energy calculations: some confusion about options

[Ryan Muraglia]

Dear GROMACS users,

I am attempting to carry out relative alchemical free energy calculations
for amino acid mutations. Below I've reproduced an excerpt from my topology
file for a leucine to alanine mutation (generated with the pmx package):

17   N  2L2A  N 17  -0.41570014.0100
18   H  2L2A  H 18   0.271900 1.0080
19  CT  2L2A CA 19  -0.05180012.0100
   CT   0.03370012.0100
20  H1  2L2A HA 20   0.092200 1.0080
   H1   0.082300 1.0080
21  CT  2L2A CB 21  -0.11020012.0100
   CT  -0.18250012.0100
22  HC  2L2AHB1 22   0.045700 1.0080
   HC   0.060300 1.0080
23  HC  2L2AHB2 23   0.045700 1.0080
   HC   0.060300 1.0080
24  CT  2L2A CG 24   0.35310012.0100
   HC   0.060300 1.0080
25  HC  2L2A HG 25  -0.036100 1.0080
 DUM_HC   0.00 1.
26  CT  2L2ACD1 26  -0.41210012.0100
 DUM_CT   0.00 1.
27  HC  2L2A   HD11 27   0.10 1.0080
 DUM_HC   0.00 1.
28  HC  2L2A   HD12 28   0.10 1.0080
 DUM_HC   0.00 1.
29  HC  2L2A   HD13 29   0.10 1.0080
 DUM_HC   0.00 1.
30  CT  2L2ACD2 30  -0.41210012.0100
 DUM_CT   0.00 1.
31  HC  2L2A   HD21 31   0.10 1.0080
 DUM_HC   0.00 1.
32  HC  2L2A   HD22 32   0.10 1.0080
 DUM_HC   0.00 1.
33  HC  2L2A   HD23 33   0.10 1.0080
 DUM_HC   0.00 1.
34   C  2L2A  C 34   0.59730012.0100
35   O  2L2A  O 35  -0.56790016.

My plan is to follow the general process of a three step alchemical
transformation: decharging the changing atoms, swapping the Lennard-Jones
terms, then recharging the new atoms. Looking at the available free energy
options, I'm unsure of how to proceed, and I want to clarify the function
of the couple-lambda0 and 1 flags. Here is one scheme I've thought of.
Please let me know if it is appropriate, or if I've made an error somewhere.

Step 1: use an unmutated leucine topology (not reproduced here, but
essentially same as above, without B state specified and with L2A renamed
to LEU) to calculate the decharging step.
Parameters are: couple-lambda0 = vdw-q, couple-lambda1 = vdw, coul_lambdas
= 0.0 0.5 1.0 (normally I will use more lambdas, but for clarity, I'm only
specifying three here).
My intention here is for the 0th state to be a fully interacting leucine,
and the 2nd state to be a decharged leucine. Is this correct? Is specifying
couple-lambda1 = vdw sufficient, or do I have to specify a B state in the
topology with explicit 0 charges?

Step 2: use the mutated topology above with the following parameters:
couple-lambda0 = vdw, couple-lambda1 = vdw-q,
coul_lambdas = 0.0 0.0 0.0 0.5 1.0
vdw_lambdas  = 0.0 0.5 1.0 1.0 1.0
bonded and mass lambdas same as vdw.
Here my intention is for the 0th state to be the same uncharged leucine
from before, then 2nd state to be the uncharged alanine, then the 4th state
to be the fully interacting alanine.

Again, I want to confirm that my understanding of the free energy options
is appropriate, and this calculation scheme will accomplish what I
described above.

Thank you for reading, and for any advice you can offer!

-- 
Ryan Muraglia
rmurag...@gmail.com
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Re: [gmx-users] Simulation terminated after 260 ns of simulation

[Szilárd Páll]

There is a small chance that your crashes are caused by a rare bug that
could affect runs where the GPU is shared by multiple ranks. This was fixed
in 5.0.6, I suggest updating your installation.

For more details see the release notes:
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

Cheers,

--
Szilárd

On Tue, Jan 19, 2016 at 12:53 PM, anu chandra  wrote:

> Dear Gromcas users,
>
> I have been carrying out a simulation of protein in POPC membrane.  After
> the successful completion of about 260 ns, simulation terminated with the
> following error.
>
> ***
> Reading checkpoint file 16md.cpt generated: Sun Jan 17 06:38:52 2016
>
>
> Using 4 MPI processes
> Using 6 OpenMP threads per MPI process
>
> 2 GPUs detected on host tesla68:
>   #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>   #1: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>
> 2 GPUs auto-selected for this run.
> Mapping of GPUs to the 2 PP ranks in this node: #0, #1
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
> WARNING: This run will generate roughly 5432 Mb of data
> starting mdrun 'Title'
> 13300 steps, 266000.0 ps (continuing from step 12050, 241000.0 ps).
>
> NOTE: Turning on dynamic load balancing
>
>
> ---
> Program gmx_mpi, VERSION 5.0.5
> Source code file: /tmp/gromacs-5.0.5/src/gromacs/mdlib/pme.c, line: 754
>
> Fatal error:
> 35983 particles communicated to PME rank 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> 
>
>
> I am using the following input parameters for simulation. I also used
> flat-bottom position restrain  during simulation.
>
> **
> define  = -DPOSRES -DMD -DPOSRES_POT
> ;
> integrator  = md
> dt  = 0.002
> nsteps  = 50
> tinit   = 0
> init-step   = 0
> ;
> nstlog  = 1000
> nstxout = 2
> nstvout = 2
> nstfout = 2
> nstcalcenergy   = 100
> nstenergy   = 1000
> nstxout-compressed  = 4000
> compressed-x-grps   = System
> ;
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> coulombtype = pme
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ;
> pbc = xyz
> ;
> tcoupl  = Nose-Hoover
> tc_grps = Protein POPC K_CL_SOL
> tau_t   = 1.01.0 1.0
> ref_t   = 305.0305.0305.0
> ;
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> ;
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_POPC K_CL_SOL
> ;
> refcoord_scaling= com
>
>
> **
>
> I just wonder why Gromcas detected an improper system equilibration after
> 250 ns of simulation, though the system looks fine. Can anybody help me to
> get rid off the error here.
>
>
> Many thanks in advance
>
> Anu
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[gmx-users] Error estimate for order parameter

[m g]

Dear all,How can i calculate the error bar for order parameter in gromacs? 
which command must be use?

many thanks
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Re: [gmx-users] disabling pbc while using trjconv

[Peter Stern]

First try the trjconv option -pbc no jump.

Peter

Sent from my iPad

> On 20 בינו׳ 2016, at 19:50, Irem Altan  wrote:
> 
> Hi,
> 
> When generating trajectories with trjconv in .pdb format, is it possible to 
> have the coordinates unwrapped? What I mean by this is to have coordinates 
> the way they were in the original protein .pdb file: not wrapped into the 
> unit cell (so that the protein is a single piece).
> 
> Best,
> Irem
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Re: [gmx-users] GROMACS performance with an NVidia Tesla k40c

[Michail Palaiokostas Avramidis]

Hi,

thanks for your answer. :) I tried to attach in the previous email
the log file but for some reason it never arrived on the list. Actually I 
searched a bit more and the speed up reaches the theoretical maximum reported 
by Nvidia so probably I shouldn't be greedy. The log file cleared of all the 
reference notes and thermodynamic output is: 

Log file opened on Tue Jan 19 18:48:55 2016
Host: -  pid: 1215  rank ID: 0  number of ranks:  1

GROMACS:  gmx mdrun, VERSION 5.1.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -v -deffnm npt-ini -gpu_id 0

GROMACS version:VERSION 5.1.1
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:enabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  AVX_256
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  disabled
TNG support:enabled
Tracing support:disabled
Built on:   Tue Jan 19 18:00:50 GMT 2016
Built by:   - [CMAKE]
Build OS/arch:  Linux 3.13.0-74-generic x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2643 0 @ 3.30GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.8.4
C compiler flags:-mavx-Wextra -Wno-missing-field-initializers 
-Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value 
-Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
-Wno-array-bounds 
C++ compiler:   /usr/bin/c++ GNU 4.8.4
C++ compiler flags:  -mavx-Wextra -Wno-missing-field-initializers 
-Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  -Wno-array-bounds 
Boost version:  1.55.0 (internal)
CUDA compiler:  /usr/local/cuda-7.5/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
CUDA compiler 
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
 
;-mavx;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
CUDA driver:7.50
CUDA runtime:   7.50


Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2643 0 @ 3.30GHz
Family:  6  model: 45  stepping:  7
CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
  GPU info:
Number of GPUs detected: 2
#0: NVIDIA Tesla K40c, compute cap.: 3.5, ECC: yes, stat: compatible
#1: NVIDIA Quadro 2000, compute cap.: 2.1, ECC:  no, stat: compatible

For optimal performance with a GPU nstlist (now 10) should be larger.
The optimum depends on your CPU and GPU resources.
You might want to try several nstlist values.
Changing nstlist from 10 to 40, rlist from 1.2 to 1.235

Input Parameters:
   integrator = md
   tinit  = 0
   dt = 0.002
   nsteps = 5000
   init-step  = 0
   simulation-part= 1
   comm-mode  = Linear
   nstcomm= 100
   bd-fric= 0
   ld-seed= 555955623
   emtol  = 10
   emstep = 0.01
   niter  = 20
   fcstep = 0
   nstcgsteep = 1000
   nbfgscorr  = 10
   rtpi   = 0.05
   nstxout= 500
   nstvout= 500
   nstfout= 500
   nstlog = 500
   nstcalcenergy  = 100
   nstenergy  = 500
   nstxout-compressed = 500
   compressed-x-precision = 1000
   cutoff-scheme  = Verlet
   nstlist= 40
   ns-type= Grid
   pbc= xyz
   periodic-molecules = FALSE
   verlet-buffer-tolerance= 

[gmx-users] disabling pbc while using trjconv

[Irem Altan]

Hi,

When generating trajectories with trjconv in .pdb format, is it possible to 
have the coordinates unwrapped? What I mean by this is to have coordinates the 
way they were in the original protein .pdb file: not wrapped into the unit cell 
(so that the protein is a single piece).

Best,
Irem
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[gmx-users] custom force constants

[Irem Altan]

Hi,

I am trying to create a position restraint file with custom force constants. 
The file looks like as follows:

; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type  fx  fy  fz
1 2271 2271 2271
5 2202 2202 2202
7 2160 2160 2160
10 2523 2523 2523

etc.

However, when I’m trying to create an executable with grompp, I get the 
following error:

Fatal error:
Invalid position restraint type 2271
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The documentation does not list this error as far as I can see. Does this mean 
that intermediate values are not allowed? If so, what are the allowed values 
and what do they correspond to?

Best,
Irem
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Re: [gmx-users] custom force constants

[Mark Abraham]

Hi,

Table 5.5. of the manual shows the required formats - and the hint in the
comment in your file is accurate also. You need to specify a "type" field
(often 1).

Mark

On Wed, Jan 20, 2016 at 4:11 PM Irem Altan  wrote:

> Hi,
>
> I am trying to create a position restraint file with custom force
> constants. The file looks like as follows:
>
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom  type  fx  fy  fz
> 1 2271 2271 2271
> 5 2202 2202 2202
> 7 2160 2160 2160
> 10 2523 2523 2523
>
> etc.
>
> However, when I’m trying to create an executable with grompp, I get the
> following error:
>
> Fatal error:
> Invalid position restraint type 2271
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> The documentation does not list this error as far as I can see. Does this
> mean that intermediate values are not allowed? If so, what are the allowed
> values and what do they correspond to?
>
> Best,
> Irem
> --
> Gromacs Users mailing list
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Re: [gmx-users] HREMD output

[Mark Abraham]

Hi,


On Wed, Jan 20, 2016 at 3:07 PM Shyno Mathew  wrote:

> Dear all,
>
> Using demux.pl script, I created the co-ordinate trajectories.


Unlike some other MD packages, GROMACS REMD trajectories are written such
that they are continuous with respect to ensemble index. So only demux if
you want continuous with respect to replica index.

When I plot
> the rmsd for the lowest replica, I see huge jumps (0.4 nm to 0.6nm) at few
> steps.


If you've demuxed, your trajectory should be free of jumps, so this sounds
like a normal issue of dealing with periodicity (
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
)


> To explain this behavior I need to find out the temperature at each
> step.
>
> Now to see the temperature for each step, I need to look for 0 in each row
> in replica_temp.xvg and see which column 0 belongs to. Is this correct?
>
> Following are the first three lines of the replica_temp.xvg file. I have 32
> replicas, and there is no exchange in the first 5ns. If I look at step3
> (frame 5002), replica 0 is in column 4, meaning replica 0 has the
> temperature of replica 2?
>

Probably so. I forget what the script does for the two .xvg files it
writes, but you can work it out by inspecting your .log files to see what
exchanges actually occured over the first few exchange intervals.

Mark


>
> 0   0123456789
> 10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
> 25   26   27   28   29   30   31
> 50000214356879
> 10   11   12   13   14   15   16   18   17   19   20   22   21   24   23
> 26   25   27   28   30   29   31
> 50021204356879
> 10   11   12   13   14   15   16   18   17   19   21   22   20   25   23
> 27   24   26   28   30   29   31
>
>
> thanks,
> Shyno
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
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Re: [gmx-users] disabling pbc while using trjconv

[Irem Altan]

It did the trick, thanks!

Best,
Irem

> On Jan 20, 2016, at 1:04 PM, Peter Stern  wrote:
> 
> First try the trjconv option -pbc no jump.
> 
> Peter
> 
> Sent from my iPad
> 
>> On 20 בינו׳ 2016, at 19:50, Irem Altan  wrote:
>> 
>> Hi,
>> 
>> When generating trajectories with trjconv in .pdb format, is it possible to 
>> have the coordinates unwrapped? What I mean by this is to have coordinates 
>> the way they were in the original protein .pdb file: not wrapped into the 
>> unit cell (so that the protein is a single piece).
>> 
>> Best,
>> Irem
>> -- 
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Re: [gmx-users] pdb2gmx, chain and segment names in the output pdb

[Alexey Shvetsov]

Maxim Igaev писал 13-01-2016 19:51:

Dear Gromacs users,

I have a large molecular complex consisting of many identical monomers.
I constructed a pdb file for it using VMD and assigned each monomer
a segment name (A0, A1, A2 etc.). The chain name was however always
the same - A. Then I created the topology for it using pdb2gmx.


This should be fixed GROMACS master branch. It will not preserve segid, 
but it will add chain ids for all chains (up to 62 chains).




In the output pdb file, however, all segment names have disappeared
and the chain names have changed - instead of A for each monomer, I
now have A, B, C, D etc for the first ~20 monomers and then simply
nothing for the rest of the monomers.

Is there a way to make pdb2gmx preserve segment/chain names while
creating a topology file?

I need my initial naming since I want to postprocess my trajectories
in VMD again.

Thanks a lot in advance!

Cheers,
Maxim


--
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexx...@gmail.com
mailto:ale...@omrb.pnpi.spb.ru
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Re: [gmx-users] custom force constants

[Irem Altan]

Hi,

I can’t believe I overlooked something that simple. Thanks!

Best,
Irem

> On Jan 20, 2016, at 10:19 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> Table 5.5. of the manual shows the required formats - and the hint in the
> comment in your file is accurate also. You need to specify a "type" field
> (often 1).
> 
> Mark
> 
> On Wed, Jan 20, 2016 at 4:11 PM Irem Altan  wrote:
> 
>> Hi,
>> 
>> I am trying to create a position restraint file with custom force
>> constants. The file looks like as follows:
>> 
>> ; In this topology include file, you will find position restraint
>> ; entries for all the heavy atoms in your original pdb file.
>> ; This means that all the protons which were added by pdb2gmx are
>> ; not restrained.
>> 
>> [ position_restraints ]
>> ; atom  type  fx  fy  fz
>> 1 2271 2271 2271
>> 5 2202 2202 2202
>> 7 2160 2160 2160
>> 10 2523 2523 2523
>> 
>> etc.
>> 
>> However, when I’m trying to create an executable with grompp, I get the
>> following error:
>> 
>> Fatal error:
>> Invalid position restraint type 2271
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> The documentation does not list this error as far as I can see. Does this
>> mean that intermediate values are not allowed? If so, what are the allowed
>> values and what do they correspond to?
>> 
>> Best,
>> Irem
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

Hi Justin and Marco,

Thanks for your reply. I get this behaviour when I specify the default NH3+
and COO- termini through -ter, as well as when I don't use the -ter flag.
Selecting the COOH terminus type removed the warning for the C-terminus,
but selecting the NH2 terminus type did't remove the warning for the
N-terminus. That's not a very physiological state, however.

Can anyone replicate this error?

Kind regards

Dries
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[gmx-users] find hbond between different groups during simulation

[Mahboobe Sadr]

Dear all,

I want to find hydrogen bonds between waters and The protein. since in each
frame I selected some specifc waters, I want to find hydrogen bonds during
simulation for different waters(which are in the pore of the protein) and
the protein.
 as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
couldn't find the hbond i want.

Thank you in advance.
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Re: [gmx-users] Gromacs Tutorial

[Peter Stern]

The only thing that you can do about this is to learn from the experience and 
in the future, copyright everything that you create and distribute.  Then 
nobody can "plagiarize" your work without your permission.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Tuesday, January 19, 2016 3:01 PM
To: mdgroup; Discussion list for GROMACS users
Subject: [gmx-users] Gromacs Tutorial

Hey :)

As some of you know, some years ago I developed an extensive Gromacs tutorial 
(at the University of Utrecht). That work has caught they eye of educators, and 
now the tutorial is published as an educational paper! Just kind of funny that 
I'm not an author.
For those interested:

http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract

Enjoy!

Tsjerk

--
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Re: [gmx-users] Gromacs Tutorial

[Tsjerk Wassenaar]

Hey Guys,

I did not mean to make this a scandal of some sort! If you think anything
of it like that, please contact me directly.

The paper is interesting! That's a reason to share it.

I also need to note (now certainly) that the paper does not discuss the
didactical issues and considerations that made my tutorial the way it was,
but the paper addresses the changes the group made to it afterwards. I
would have loved to be part of that, and I think it would have been nice to
add my few cents on the underlying principles which are still at the core
of the tutorial. But this is the tutorial it is now, and that's the work of
Joao, Adrien and Alexandre (who are dear to me).

Joao (Henriques) hits the nail: Interesting paper/tutorial, Work of the
Insitute, they acknowledged me.

Case closed. Read the paper, tell your students.

Cheers,

Tsjerk



On Wed, Jan 20, 2016 at 11:45 AM, João Henriques <
joao.henriques.32...@gmail.com> wrote:

> Well... he did get acknowledged :) Plus, I doubt anyone here besides Tsjerk
> and his old colleagues knows who "legally" has the right to his work. What
> I mean is that, for example, in my current institution, the student has the
> right to products of his/her labour, but in other countries the institution
> and/or the research group owns it, and so they can do as they please with
> it (more or less, but you get the point).
>
> Anyway, thanks for the link, this article will go straight into the hands
> of my new master's student, who is just starting in this field of research.
>
> Best regards,
> /J
>
>
> On Wed, Jan 20, 2016 at 11:00 AM, Peter Stern 
> wrote:
>
> > The only thing that you can do about this is to learn from the experience
> > and in the future, copyright everything that you create and distribute.
> > Then nobody can "plagiarize" your work without your permission.
> >
> > Peter
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
> > Wassenaar
> > Sent: Tuesday, January 19, 2016 3:01 PM
> > To: mdgroup; Discussion list for GROMACS users
> > Subject: [gmx-users] Gromacs Tutorial
> >
> > Hey :)
> >
> > As some of you know, some years ago I developed an extensive Gromacs
> > tutorial (at the University of Utrecht). That work has caught they eye of
> > educators, and now the tutorial is published as an educational paper!
> Just
> > kind of funny that I'm not an author.
> > For those interested:
> >
> > http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
> >
> > Enjoy!
> >
> > Tsjerk
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
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[gmx-users] question on editconf

[Sotirios Dionysios I. Papadatos]

I am trying to change the orientation of a protein embedded in a protein. I am 
using the command editconf -rotate. The output is only the protein without the 
membrane. My question is if there is a way to do a rotation of the protein in 
regard to the membrane (I am using an index file). Thanks in advance
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[gmx-users] Gromacs Tutorial

[João Rodrigues]

Dear all,

Those of you who read the paper will realize that we do acknowledge Tsjerk,
and keep doing so on the web pages of the material, but there are reasons
we considered sufficient to justify the author listing on the paper.

However, since Tsjerk knows me and the other authors (them actually rather
well) since at least 2008, I (we) will sort this issue privately.

Cheers,

João
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Re: [gmx-users] Gromacs Tutorial

[João Henriques]

Well... he did get acknowledged :) Plus, I doubt anyone here besides Tsjerk
and his old colleagues knows who "legally" has the right to his work. What
I mean is that, for example, in my current institution, the student has the
right to products of his/her labour, but in other countries the institution
and/or the research group owns it, and so they can do as they please with
it (more or less, but you get the point).

Anyway, thanks for the link, this article will go straight into the hands
of my new master's student, who is just starting in this field of research.

Best regards,
/J


On Wed, Jan 20, 2016 at 11:00 AM, Peter Stern 
wrote:

> The only thing that you can do about this is to learn from the experience
> and in the future, copyright everything that you create and distribute.
> Then nobody can "plagiarize" your work without your permission.
>
> Peter
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
> Wassenaar
> Sent: Tuesday, January 19, 2016 3:01 PM
> To: mdgroup; Discussion list for GROMACS users
> Subject: [gmx-users] Gromacs Tutorial
>
> Hey :)
>
> As some of you know, some years ago I developed an extensive Gromacs
> tutorial (at the University of Utrecht). That work has caught they eye of
> educators, and now the tutorial is published as an educational paper! Just
> kind of funny that I'm not an author.
> For those interested:
>
> http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
>
> Enjoy!
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
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[gmx-users] gmx energy block averaging

[Andreas Mecklenfeld]

Dear Gromacs-users,

I've a question regarding the gmx energy functionality. I want to 
perform a block averaging with a prescribed number of data points in 
each block.


The manual section of this command says

"Note that in most cases the energy files contains averages over all MD 
steps, or over many more points than the number of frames in energy file."


which is in accordance with the information given for the 
nstenergy-parameter


"Note that the exact sums and fluctuations over all MD steps modulo 
nstcalcenergy are stored in the energy file, so g_energy can report 
exact energy averages and fluctuations also when nstenergy>1"


I'm aware that I can give the number of blocks for the gmx energy 
evaluation with -nbmin respectively -nbmax, though I'm uncertain about 
the number of data points gmx energy actually uses for the block 
averaging. Say, I've performed  1e6 steps with nstenergy = 1000 and I 
want 5000 points per block - do I need 200 blocks in total?


Thanks,
Andreas


--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

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[gmx-users] HREMD output

[Shyno Mathew]

Dear all,

Using demux.pl script, I created the co-ordinate trajectories. When I plot
the rmsd for the lowest replica, I see huge jumps (0.4 nm to 0.6nm) at few
steps. To explain this behavior I need to find out the temperature at each
step.

Now to see the temperature for each step, I need to look for 0 in each row
in replica_temp.xvg and see which column 0 belongs to. Is this correct?

Following are the first three lines of the replica_temp.xvg file. I have 32
replicas, and there is no exchange in the first 5ns. If I look at step3
(frame 5002), replica 0 is in column 4, meaning replica 0 has the
temperature of replica 2?

0   0123456789
10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
25   26   27   28   29   30   31
50000214356879
10   11   12   13   14   15   16   18   17   19   20   22   21   24   23
26   25   27   28   30   29   31
50021204356879
10   11   12   13   14   15   16   18   17   19   21   22   20   25   23
27   24   26   28   30   29   31


thanks,
Shyno

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
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