[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

[ABEL Stephane]

Hi Justin

I obtained the following error with the following command and the mdp mentioned 
below 

gmx mdrun -s 1_OGNG_GLYCAM_SPE_GMX.tpr -rerun 1_OGNG_Amber.pdb

Thank you 

Stéphane

--
Program: gmx mdrun, version 2018.1
Source file: src/programs/mdrun/runner.cpp (line 736)

Fatal error:
The .mdp file specified an energy mininization or normal mode algorithm, and
these are not compatible with mdrun -rerun

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

>> You also shouldn't use a minimizer when doing a zero-point energy. Use the 
>> md integrator.
OK I try your suggestion

--

And the mdp 

Message: 1
Date: Thu, 23 Apr 2020 06:18:33 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS mdp file for doing a single point
energy after acpype conversion
Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 4/23/20 5:42 AM, ABEL Stephane wrote:
> Deal all,
>
> I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 
> force fiedl  into the GROMACS format. acpype works well for this task. But I 
> would like to check if the conversion is correctly done by performing single 
> point energy (SPE) calculations with Amber and GROMACS codes and thus 
> computes the energy differences  for the bonded and non bonded terms
>
> For the former test I using the prmtop and inpcrd files generated with tleap 
> and sander with the minimal commands below
>
> | mdin Single point
> 
> imin=0,
> maxcyc=0,
> ntmin=2,
> ntb=0,
> igb=0,
> cut=999
> /
>
> But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp 
> parameters that can be used for doing the same task. I I used  the minimal 
> file below The bonded energy terms are very similar between the two codes but 
> not the non bonded terms
>
> integrator  = steep ; Algorithm (steep = steepest descent 
> minimization)
> emtol   = 1000.0; Stop minimization when the maximum force < 
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Minimization step size
> nsteps  = 0   ; Maximum number of (minimization) steps to perform 
> (should be 5)
>
> ; Parameters describing how to find the neighbors of each atom and how to 
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long 
> range forces
> cutoff-scheme   = Group   ; Buffered neighbor searching
> ns_type = grid  ; Method to determine neighbor list (simple, grid)
> coulombtype = Cut-off   ; Treatment of long range electrostatic 
> interactions
> rcoulomb= 0   ; Short-range electrostatic cut-off
> rvdw= 0   ; Short-range Van der Waals cut-off
> rlist   = 0
> pbc = no   ; P
> continuation = yes
>
> I also also notice that a tpr generated with this mdp can not be used with 
> -rerun argument so how I can compute a SPE equivalent to Sander

Why is it incompatible with mdrun -rerun? Do you get an error?

You also shouldn't use a minimizer when doing a zero-point energy. Use
the md integrator.

-Justin
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[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

[ABEL Stephane]

Deal all, 

I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 
force fiedl  into the GROMACS format. acpype works well for this task. But I 
would like to check if the conversion is correctly done by performing single 
point energy (SPE) calculations with Amber and GROMACS codes and thus computes 
the energy differences  for the bonded and non bonded terms

For the former test I using the prmtop and inpcrd files generated with tleap 
and sander with the minimal commands below 

| mdin Single point

imin=0,
maxcyc=0,
ntmin=2,
ntb=0,
igb=0,
cut=999
/

But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp 
parameters that can be used for doing the same task. I I used  the minimal file 
below The bonded energy terms are very similar between the two codes but not 
the non bonded terms

integrator  = steep ; Algorithm (steep = steepest descent minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Minimization step size
nsteps  = 0   ; Maximum number of (minimization) steps to perform 
(should be 5)

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long 
range forces
cutoff-scheme   = Group   ; Buffered neighbor searching
ns_type = grid  ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off   ; Treatment of long range electrostatic interactions
rcoulomb= 0   ; Short-range electrostatic cut-off
rvdw= 0   ; Short-range Van der Waals cut-off
rlist   = 0
pbc = no   ; P
continuation = yes

I also also notice that a tpr generated with this mdp can not be used with 
-rerun argument so how I can compute a SPE equivalent to Sander

Thanks in advance for your help and suggestions


Stéphane

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[gmx-users] Some atoms are not properly rotated with gmx_editconf

[ABEL Stephane]

Hello 

I would like my gramicidin A channel along the z axis. So I use the following 
commands in a bash script

## Select a group for determining the system size: System : 0 
## Select group for the determining the orientation ! GramicidinA : 15
## Select a group that you want to align: TRP12_CA_DLEU_32_CA : 16
## Select a group for output: System : 0

## Align the Channel along the z axis 

echo 0 15 16 0 > vector.txt


  gmx_mpi editconf -f 1JNO_GramicidineA_pep_em_step0.pdb -o 
1JNO_GramicidineA_pep_em_step0_reoriented_along_Zaxis.pdb -princ -rotate -0 90 
0 -align 0 90 0 -n System.ndx -box 5.0 5.0 5.0 -center 2.5 2.5 2.5 -resnr 1 < 
vector.txt

## Center the channel

mpirun -np 1 gmx_mpi trjconv -f 
1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis.pdb -s 
1JNO_GramicidineA_pep_em_step0.tpr -pbc mol -ur compact -center -o 
1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb -n System.ndx

The problem is that the channel is well aligned along the z axis but "not" the 
TRP12_CA_DLEU_32_CA atoms used for the vector. 

How to resolve this ?

You could download the pdb file (below) and see what I mean with pymol

https://www.dropbox.com/s/l5crrpxsy3fak6e/1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb?dl=0

Best regards 

Stéphane

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[gmx-users] How to obtain the number of residue per turn with GROMACS ?

[ABEL Stephane]

Hello, 

I would like to obtain the time serie of the number of residues per turn with 
GROMACS for a given peptide ? Is it possible to obtain this property with a 
GROMACS tool ? If yes, how ?

Thank you 

Stéphane
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[gmx-users] Recreating newer TPRs for old Gromacs (Jernej Zidar)

[ABEL Stephane]

Hello 

If you only need the parameters of the molecules (e.g. list of bond, atom 
masses and charges) you could build  a fake tpr with a minimal list of 
parameters (for instance used for minimization) and use an the desired old 
version of grompp (Gromacs 5.0.3).  

Stéphane

--

Message: 1
Date: Thu, 26 Sep 2019 11:34:29 +0800
From: Jernej Zidar 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Recreating newer TPRs for old Gromacs
Message-ID:

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

Dear all,

For the purpose of a project I am trying to recreate TPRs so I can use them
with an older version of Gromacs. The TPR files in question are:
- ion channel:
https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseA.tar.gz
- lignocellulose:
https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseB.tar.gz

The two files were prepared in Gromacs 5.1.4 but I would like to use them
with Gromacs 5.0.3. I was able to output the relevant mdp parameters
and the initial structure but I have major issues with the forcefield
parameters. Is there a way to "extract" them from the TPR files or I should
contact the original authors instead?

Thanks in advance,
Jernej Zidar


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[gmx-users] Subject: RAM usage of gmx msd5

[ABEL Stephane]

Hello

Did you try to compute the msd for only few atoms (for instance phosphorus), 
the COM of each lipid or use different segments of your trajectory ? This 
approach is sometime used.

Stéphane

--

Message: 2
Date: Tue, 17 Sep 2019 08:46:38 +0200
From: Martin Kern 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] RAM usage of gmx msd
Message-ID: <75551d1f-9cdf-ea8d-ac2d-6576b548d...@uni-konstanz.de>
Content-Type: text/plain; charset=utf-8; format=flowed

Hello everyone.

I simulated a cell membrane and would like to calculate lateral
diffusion of lipids. I tried this using the gmx msd command.
Unfortunately this uses enormous amounts of RAM. The process runs
without error until it is killed by the operating system. No output file
is created at that time.

The membrane contains around 400 lipids and I simulated for 1100ns which
is 22 frames. The total size of the xtc file is around 150 GB. I use
GROMACS 2016.4 with GPU support. The command I used was:
gmx msd -s mdrun.tpr -f mdrun.xtc -n key_atoms.ndx -lateral z -o
lateraal_diffusion.xvg

I found an old email that also mentions the high RAM usage of gmx msd
but it didn't get a reply.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118014.html

I also tried reducing the RAM usage by creating a trajectory that only
includes the key atoms. This attempt resulted in a segmentation fault.
Here is what I tried:
gmx trjconv -f mdrun.xtc -n key_atoms.ndx -o mdrun_key_atoms.xtc
gmx convert-tpr -f mdrun.tpr -n key_atoms.ndx -o mdrun_key_atoms.tpr
gmx msd -s mdrun_key_atoms.tpr -f mdrun_key_atoms.xtc -n key_atoms.ndx
-lateral z -o lateraal_diffusion.xvg

I'm grateful for any suggestion.

Best regards
Martin Kern



--

Message: 3
Date: Tue, 17 Sep 2019 14:43:28 +0530
From: Navneet Kumar Singh 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration Problem.
Message-ID:

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

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.





*Energy  Average   Err.Est. RMSD
Tot-Drift---Pressure
  0.261272 0.49  49.10611.55678  (bar)*


*Density213.361   0.58   1.18799
   4.08348 (kg/m^3)*


*Temperature   300.002   0.04  2.38265
-0.0854606  (K)*

*---*

*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 )
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*


 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  


 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.


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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 55

[ABEL Stephane]

Hello 

Did you try to compute the msd for only few atoms (for instance phosphorus), 
the COM of each lipid or use different segments of your trajectory ? This 
approach is sometime used. 

Stéphane

--

Message: 2
Date: Tue, 17 Sep 2019 08:46:38 +0200
From: Martin Kern 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] RAM usage of gmx msd
Message-ID: <75551d1f-9cdf-ea8d-ac2d-6576b548d...@uni-konstanz.de>
Content-Type: text/plain; charset=utf-8; format=flowed

Hello everyone.

I simulated a cell membrane and would like to calculate lateral
diffusion of lipids. I tried this using the gmx msd command.
Unfortunately this uses enormous amounts of RAM. The process runs
without error until it is killed by the operating system. No output file
is created at that time.

The membrane contains around 400 lipids and I simulated for 1100ns which
is 22 frames. The total size of the xtc file is around 150 GB. I use
GROMACS 2016.4 with GPU support. The command I used was:
gmx msd -s mdrun.tpr -f mdrun.xtc -n key_atoms.ndx -lateral z -o
lateraal_diffusion.xvg

I found an old email that also mentions the high RAM usage of gmx msd
but it didn't get a reply.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118014.html

I also tried reducing the RAM usage by creating a trajectory that only
includes the key atoms. This attempt resulted in a segmentation fault.
Here is what I tried:
gmx trjconv -f mdrun.xtc -n key_atoms.ndx -o mdrun_key_atoms.xtc
gmx convert-tpr -f mdrun.tpr -n key_atoms.ndx -o mdrun_key_atoms.tpr
gmx msd -s mdrun_key_atoms.tpr -f mdrun_key_atoms.xtc -n key_atoms.ndx
-lateral z -o lateraal_diffusion.xvg

I'm grateful for any suggestion.

Best regards
Martin Kern



--

Message: 3
Date: Tue, 17 Sep 2019 14:43:28 +0530
From: Navneet Kumar Singh 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration Problem.
Message-ID:

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

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.





*Energy  Average   Err.Est. RMSD
Tot-Drift---Pressure
  0.261272 0.49  49.10611.55678  (bar)*


*Density213.361   0.58   1.18799
   4.08348 (kg/m^3)*


*Temperature   300.002   0.04  2.38265
-0.0854606  (K)*

*---*

*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 )
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*


 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  


 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.


--

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[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

[ABEL Stephane]

Hello 

there are not parameters and RESP charges for standalone residue such as Arg in 
GROMACS. So you will have to construct a rtp file for this residue and derive 
the corresponding RESP charges yourself. You could also do a quick in 
literature to see if some have already done the job for you. 

Good luck

Stefane

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Re: [gmx-users] Calculating electron density profile of a lipid bilayer system

[ABEL Stephane]

Hello 

>> Could you please give an example on how to modify the number of electrons? 
>> Do I need to use the itp file?
As it is said in the gmx density -h 

"The first line contains the number of lines to read from the file. There 
should be one line for each unique atom name in your system. The number of 
electrons for each atom is modified by its atomic partial charge."

So for instance, the CHARMM TIP3P atom have the following charges (according 
the itp) 

 1 OT  1 TIP3OH2  1 -0.83415.9994   ; qtot 
-0.834
 2 HT  1 TIP3 H1  2  0.417 1.0080   ; qtot 
-0.417
 3 HT  1 TIP3 H2  3  0.417 1.0080   ; qtot  
0.000

So in your electron.dat you should have for water, 

3
OH2 = 7.166   ---> 8 -0.834 
H1  = 1.417  -->  1 + 0.417
H2  = 1.417--> 1 + 0.417

HTH



--


Message: 4
Date: Fri, 31 May 2019 10:19:56 +0200
From: Azadeh Alavizargar 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Calculating electron density profile of a
lipid bilayer system
Message-ID:

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

Dear Stephane

Thank you very much for your reply. I am sorry, I had not noticed you have
answered before and was thinking my message has not been sent so I sent it
again.
I am sorry, but I did not get you completely. How should I take into
account the number of electrons? I thought that I just need to give the
atomic number of each element in the electron.dat file. Could you please
give an example on how to modify the number of electrons? Do I need to use
the itp file?

Thanks a lot.

Best regards,
Azadeh

On Thu, May 30, 2019 at 2:50 PM ABEL Stephane  wrote:

> Hello
>
> I gave you a response few days ago
>
> For the calculations of the EDP you have to take into account of the
> charges of the atom (it is mentioned at the end of density tool ("known
> issue")) . So modify the number of electrons to have the "real" electron
> numbers in you electron.dat file accordingly.
>
> HTH
>
> --
>
> Message: 2
> Date: Thu, 30 May 2019 09:55:18 +0200
> From: Azadeh Alavizargar 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Fwd: Calculating electron density profile of a
> lipid   bilayer system
> Message-ID:
> <
> calmoi-yg2ber7v1xpwmpsawsoy+bptw1y88or3zf++bowoa...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Gromacs users
>
> I am trying to calculate the electron density profiles of a lipid bilayer
> system. However I am not getting the correct profile. I would appreciate it
> a lot if you can help me.
>
> Following is the procedure I go through:
>
> 1- first I create a ndx file to select the resnames:
>
> gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
> '(resname DPPC TIP3)'
>
> 2- Then I created the electron.dat file including all the atoms (including
> hydrogens) of the selected atoms. The first lines look like this:
> 208
> OH = 8
> H1 = 1
> H2 = 1
> N = 7
> C13 = 6
> H13A = 1
> H13B = 1
> H13C = 1
> C14 = 6
> H14A = 1
> H14B = 1
> H14C = 1
> C15 = 6
> ...
>
> 3- Then I use gmx density in order to calculate the electron density of the
> selected resnames:
>
> gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
>  density_traj_center.xvg -dens electron -ei electron.dat -center -relative
>
> However,  what I get is not similar to the ones in papers:
> Best regards,
> Azadeh
> [image: image.png]
>
> --
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> send a mail to gmx-users-requ...@gromacs.org.
>


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End of gromacs.org_gmx-users Digest, Vol 181, Issue 82
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Re: [gmx-users] Calculating electron density profile of a lipid bilayer system

[ABEL Stephane]

Hello 

I gave you a response few days ago 

For the calculations of the EDP you have to take into account of the charges of 
the atom (it is mentioned at the end of density tool ("known issue")) . So 
modify the number of electrons to have the "real" electron numbers in you 
electron.dat file accordingly.

HTH 

--

Message: 2
Date: Thu, 30 May 2019 09:55:18 +0200
From: Azadeh Alavizargar 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fwd: Calculating electron density profile of a
lipid   bilayer system
Message-ID:

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

Dear Gromacs users

I am trying to calculate the electron density profiles of a lipid bilayer
system. However I am not getting the correct profile. I would appreciate it
a lot if you can help me.

Following is the procedure I go through:

1- first I create a ndx file to select the resnames:

gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
'(resname DPPC TIP3)'

2- Then I created the electron.dat file including all the atoms (including
hydrogens) of the selected atoms. The first lines look like this:
208
OH = 8
H1 = 1
H2 = 1
N = 7
C13 = 6
H13A = 1
H13B = 1
H13C = 1
C14 = 6
H14A = 1
H14B = 1
H14C = 1
C15 = 6
...

3- Then I use gmx density in order to calculate the electron density of the
selected resnames:

gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
 density_traj_center.xvg -dens electron -ei electron.dat -center -relative

However,  what I get is not similar to the ones in papers:
Best regards,
Azadeh
[image: image.png]

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 64

[ABEL Stephane]

Hello Azadeh

For the calculations of the EDP you have to take into account of the charges of 
the atom (it is mentioned at the end of density tool ("known issue")) . So 
modify the number of electrons to have the "real" electron numbers in you 
electron.dat file accordingly.

HTH 


--

Message: 1
Date: Sat, 25 May 2019 13:21:32 +0200
From: Azadeh Alavizargar 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Calculating electron density profile of a lipid
bilayer system
Message-ID:

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

Dear Gromacs users

I am trying to calculate the electron density profiles of a lipid bilayer
system. However I am not getting the correct profile. I would appreciate it
a lot if you can help me.

Following is the procedure I go through:

1- first I create a ndx file to select the resnames:

gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
'(resname DPPC TIP3)'

2- Then I created the electron.dat file including all the atoms (including
hydrogens) of the selected atoms. The first lines look like this:
208
OH = 8
H1 = 1
H2 = 1
N = 7
C13 = 6
H13A = 1
H13B = 1
H13C = 1
C14 = 6
H14A = 1
H14B = 1
H14C = 1
C15 = 6
...

3- Then I use gmx density in order to calculate the electron density of the
selected resnames:

gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
 density_traj_center.xvg -dens electron -ei electron.dat -center -relative

However,  what I get is not similar to the ones in papers:
Best regards,
Azadeh
[image: image.png]

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Re: [gmx-users] select an atom for "only" residue with make_ndx [ Resolved ]

[ABEL Stephane]

Thanks Justin it worked. 

For the record, I have also found that 

27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33  &  rLIPIDC or aC31 | 
aC32 | aC33  &  27. 

Note For the two latter commands  the order of "r27 or rLIPIDC" is important

Thanks again 

On 5/16/19 5:44 AM, ABEL Stephane wrote:
> Thanks Justin
>
> but it does not work either
>
> LIPIDC is indeed in a group (#27)
>
> So I when typed with GMX5.1.4 or GMX2018.2
>
> LIPIDC & a C31 | a C32 | a C33  ---> Syntax error: "LIPIDC & a C31 | a C32 | 
> a C33"
> 27 & a C31 | a C32 | a C33  ---> the command works  but I selected "all" the 
> C31, C32 and C33 atoms and not only those in the LIPIDC group

Sorry, the correct syntax is:

27 & a C31 C32 C33

-Justin

> St?phane
>
> On 5/15/19 11:03 AM, ABEL Stephane wrote:
>> Hello all,
>>
>> I am currently doing simulations of a model of membranes with different 
>> types of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a 
>> group of  atoms for only the same lipid with make_ndx. Below an example
>>
>> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with 
>> the same name (C31, C32 and C33). With make_ndx I would like to have the 
>> atoms C33 and C32 for "only" the LIPIDC
>>
>> So If I do
>>
>> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 
>> lipid types.
>> So what is the exact command
> Each different [moleculetype] already has its own default group, so
> choosing atoms in LIPIDC should be as simple as:
>
> N & a C31 | a C32 | a C33
>
> where N is the group corresponding to LIPIDC.
>
> -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
>
> ==
>
>

--
==

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: 5
Date: Thu, 16 May 2019 13:55:33 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charmm 36m
Message-ID: <5a0fe974-b580-dff7-74a3-98ccd6365...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 5/15/19 3:54 PM, Coire Gavin-Hanner wrote:
> Dear Gromacs users,
>
> I am trying to use the charmm36m forcefield to simulate a protein. The most 
> recent release of charmm36 includes 36m and the ability to toggle between the 
> two. Is 36m the default state?

Yes, though it is possible to use the old C36 parameters with the
(hopefully very clear) define statement:

define = -DUSE_OLD_C36

Otherwise, the parameters used are C36m.

-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: 6
Date: Thu, 16 May 2019 18:13:34 + (UTC)
From: mary ko 
To: Discussion List for GROMACS Users

Subject: [gmx-users] number of coordinates in coordinate file does not
match   topology
Message-ID: <172035957.1411431.1558030414...@mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hello all
I want to run a simulation of a protein from PDB data bank with a ligand. It 
has two chains and I need only chain A. when I delete chain B in CHIMERA and 
try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c 
solve.pdb -p topol.top -o ions.tpr step with the error of number of coordinates 
in the solve.pdb (143982) does not match the topol.top (143983). I checked the 
.pdb file and it starts from residue 13. Do I get the error because of that 
residues not being sorted from 1, since I use the same method for the sorted 
files and they run without errors.Thank you

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[gmx-users] select an atom for "only" residue with make_ndx

[ABEL Stephane]

Thanks Justin

but it does not work either

LIPIDC is indeed in a group (#27)  

So I when typed with GMX5.1.4 or GMX2018.2

LIPIDC & a C31 | a C32 | a C33  ---> Syntax error: "LIPIDC & a C31 | a C32 | a 
C33" 
27 & a C31 | a C32 | a C33  ---> the command works  but I selected "all" the 
C31, C32 and C33 atoms and not only those in the LIPIDC group

Stéphane

On 5/15/19 11:03 AM, ABEL Stephane wrote:
> Hello all,
>
> I am currently doing simulations of a model of membranes with different types 
> of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a group of  
> atoms for only the same lipid with make_ndx. Below an example
>
> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the 
> same name (C31, C32 and C33). With make_ndx I would like to have the atoms 
> C33 and C32 for "only" the LIPIDC
>
> So If I do
>
> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 
> lipid types.
> So what is the exact command

Each different [moleculetype] already has its own default group, so
choosing atoms in LIPIDC should be as simple as:

N & a C31 | a C32 | a C33

where N is the group corresponding to LIPIDC.

-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

==


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[gmx-users] select an atom for "only" residue with make_ndx

[ABEL Stephane]

Hello all, 

I am currently doing simulations of a model of membranes with different types 
of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a group of  
atoms for only the same lipid with make_ndx. Below an example

Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the 
same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 
and C32 for "only" the LIPIDC

So If I do

rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid 
types. 

So what is the exact command

 
Thanks 

Stéphane

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[gmx-users] GROMOS 54A8 Force field

[ABEL Stephane]

With Google

http://vienna-ptm.univie.ac.at/?page_id=100

HTH

--

Message: 4
Date: Tue, 7 May 2019 09:14:42 +0200
From: Mark Abraham 
To: Discussion list for GROMACS users 
Cc: Discussion list for GROMACS users

Subject: Re: [gmx-users] GROMOS 54A8 Force field
Message-ID:

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

Hi,

I would contact the authors and ask them.

Mark

On Mon, 6 May 2019 at 11:30, Kalyanashis Jana 
wrote:

> Dear users,
> Could you please suggest me where I can get the complete package of GROMOS
> 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker (
> https://pubs.acs.org/doi/10.1021/ct300156h).
>
> Looking forward to your suggestions.
>
> Thanks in advance.
>
> Sincerely yours,
> Kalyanashis Jana
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>


--

Message: 5
Date: Tue, 7 May 2019 09:16:06 +0200
From: Mark Abraham 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Error when compiling 2019.2 with -DGMX_MPI=ON
Message-ID:

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

Hi Dallas,

The install guide tries to provide the hint to use the MPI wrapper
compilers (mpicc and mpicxx) that are installed alongside the MPI package
you installed (but maybe as part of the *mpi-dev package) . Perhaps we can
make that more clear. (And if you do, there's no need to set GMX_MPI, as
the build system will see what your intent is.) The symptoms you report
look very much like those that mpicc will handle internally.
Mark


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End of gromacs.org_gmx-users Digest, Vol 181, Issue 14
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[gmx-users] (no subject) (Soham Sarkar)

[ABEL Stephane]

Hi 

In your itp you have a "?" 

?; GENERATED BY LigParGen Server

Remove it and the problem will be solved 

PS : next time add a title in you message. 

Good luck 

-
--

Message: 1
Date: Fri, 5 Apr 2019 14:26:00 +0530
From: Soham Sarkar 
To: gmx-us...@gromacs.org
Subject: [gmx-users] (no subject)
Message-ID:

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

Dear all,
I am using GROMACS-2018. I want to simulate a system which contain
Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
the GROMPP command. I have defined this residue in aminoacids.rtp.

The error is like

"NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 918407885

WARNING 1 [file tba.itp, line 1]:
  Too few gb parameters for type ?


Couldn't find topology match for atomtype ?
Aborted (core dumped)"
 I have generated the itp file for TBA from ligpargen.

My itp file is

;
?; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;

[ atomtypes ]
  opls_135C112.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H11 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H12 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H13 1.0080 0.000A2.5E-01   1.25520E-01
  opls_159C212.0110 0.000A3.5E-01   2.76144E-01
  opls_135C312.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H31 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H32 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H33 1.0080 0.000A2.5E-01   1.25520E-01
  opls_154O415.9990 0.000A3.12000E-01   7.11280E-01
  opls_155   H41 1.0080 0.000A0.0E+00   0.0E+00
  opls_135C512.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H51 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H52 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H53 1.0080 0.000A2.5E-01   1.25520E-01

[ moleculetype ]
; Name   nrexcl
TBA   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1   opls_135  1TBAC1  1-0.304408  12.0110
 2   opls_140  1TBA   H11  1 0.098297   1.0080
 3   opls_140  1TBA   H12  1 0.086235   1.0080
 4   opls_140  1TBA   H13  1 0.111410   1.0080
 5   opls_159  1TBAC2  1 0.247098  12.0110
 6   opls_135  1TBAC3  1-0.299728  12.0110
 7   opls_140  1TBA   H31  1 0.101177   1.0080
 8   opls_140  1TBA   H32  1 0.110693   1.0080
 9   opls_140  1TBA   H33  1 0.110695   1.0080
10   opls_154  1TBAO4  1-0.550587  15.9990
11   opls_155  1TBA   H41  1 0.297574   1.0080
12   opls_135  1TBAC5  1-0.304401  12.0110
13   opls_140  1TBA   H51  1 0.098298   1.0080
14   opls_140  1TBA   H52  1 0.086234   1.0080
15   opls_140  1TBA   H53  1 0.111413   1.0080
[ bonds ]
2 1 1  0.1090 284512.000
3 1 1  0.1090 284512.000
4 1 1  0.1090 284512.000
5 1 1  0.1529 224262.400
6 5 1  0.1529 224262.400
7 6 1  0.1090 284512.000
8 6 1  0.1090 284512.000
9 6 1  0.1090 284512.000
   10 5 1  0.1410 267776.000
   1110 1  0.0945 462750.400
   12 5 1  0.1529 224262.400
   1312 1  0.1090 284512.000
   1412 1  0.1090 284512.000
   1512 1  0.1090 284512.000

[ angles ]
;  aiajak functc0c1
c2c3
2 1 3 1107.800276.144
2 1 4 1107.800276.144
2 1 5 1110.700313.800
1 5 6 1112.700488.273
5 6 7 1110.700313.800
5 6 8 1110.700313.800
5 6 9 1110.700313.800
1 510 1109.500418.400
51011 1108.500460.240
1 512 1112.700488.273
51213 1110.700313.800
51214 1110.700313.800
51215 1110.700313.800
7 6 9 1107.800276.144
6 510 1109.500418.400
3 1 4 1107.800276.144
4 1 5 1110.700313.800
3 1 5 1110.700313.800
   10 512 1109.500418.400
   141215 1  

Re: [gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS

[ABEL Stephane]

Thank you Justin, 

I "grepped" the corresponding atom types. Indeed they are in the cmap files

Stéphane

--

On 3/5/19 3:33 PM, ABEL Stephane wrote:
> Dear all,
>
> I want to performs some MD simulations of systems with a protein model with 
> D-AA and I would like to have the confirmation that the last release of the 
> CHARMM parameters for GROMACS (i.e. charmm36-nov2018.ff.tgz) contains the 
> D-CMAP terms listed in the ./stream/toppar_all36_prot_c36m_d_aminoacids.str 
> file in the original toppar_c36_jul18 archive available in the MacKerell's 
> website ?

Yes. You can grep for the relevant atom types and see that they're there.

-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: 7
Date: Wed, 6 Mar 2019 11:00:03 +0500
From: Najamuddin Memon 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] In continuous I got another warning, could
anyone help me?
Message-ID:

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

Thirdly, change constraints=all bonds instead of h bond in nvt and npt.mdp
files

On Tue, Mar 5, 2019, 11:16 PM Najamuddin Memon 
wrote:

> Do nvt and npt equillibration for 1000 ps with nxtcout, etc values 500 in
> nvt.mdp and npt.mdp file.
> Secondly, this error can be removed by changing couple intramol=yes in
> mdout.mdp file or md.mdp file.
>
> On Tue, Mar 5, 2019, 10:31 PM banijamali_fs 
> wrote:
>
>> Hi there,
>>
>> Thanks for your response, but when I went to that link, it was said to
>> put -nt 1 in command line, so when I put this I get another warning that
>> is,
>>
>> Listed nonbonded interaction between particles 1 and 29
>> at distance 2.404 which is larger than the table limit 2.200 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the
>> table-extension
>> distance in the mdp file if you are really sure that is the reason.
>>
>> So what should I do with this?
>>
>> Do anyone knows what should I exactly do?
>> --
>> 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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>>
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[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS (charmm36-nov2018.ff.tgz)?

[ABEL Stephane]

Dear all, 

I want to performs some MD simulations of systems with a protein model with 
D-AA and I would like to have the confirmation that the last release of the 
CHARMM parameters for GROMACS (i.e. charmm36-nov2018.ff.tgz) contains the 
D-CMAP terms listed in the ./stream/toppar_all36_prot_c36m_d_aminoacids.str 
file in the original toppar_c36_jul18 archive available in the MacKerell's 
website ? 

Thank you  

Stéphane

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Re: [gmx-users] Dihedral restraints

[ABEL Stephane]

Thank you Mark, 

With your example, I have finally resolved my problem and finally found that 
the dihedral restraints were not actived in my simulations :((
 
If someone is interested to know how I did for resolving my problem especially 
when you use  the files generated by CHARMM-GUI for GROMACS, do not hesitate to 
contact me directly

Thanks again

Stéphane

--

Message: 1
Date: Thu, 10 Jan 2019 07:20:26 +0100
From: Mark Abraham 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] Dihedral restraints
Message-ID:

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

Hi,

You can see a working example at

https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log

so I conclude that your restraints are inactive, somehow. Please check your
include statements, etc.

Mark


On Wed., 9 Jan. 2019, 18:05 ABEL Stephane,  wrote:

> Thanks Mark for your reply
>
> In the log and edr files I only see an "Position Rest." term. So do you
> mean that the contributions on the dihedral restrains is added in in total
> energy without additional terms in the energy output in log file and the
> edr ?
>
> Thank you in advance for the clarification.
>
> St?phane
>
>
> --
>
> Message: 3
> Date: Wed, 9 Jan 2019 12:32:31 +0100
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: Re: [gmx-users] Dihedral restraints
> Message-ID:
>  xv8qbic+t1h1cwwcnkisdfxnoja7xbot...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> IIRC that's enough, for dihedral restraints. You will see energy
> contributions from the the restraints appear in your .log and .edr files if
> the restraints are active. I don't recall if there is anything printed by
> mdrun before the simulation commences.
>
> Mark
>
> On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane 
> wrote:
>
> > Hello
> >
> > I would like to apply some dihedral restraints in different residues of
> my
> > protein during the production stage. For that I have added at the end of
> > the protein itp the section
> > [ dihedral_restraints ]. Is it enough ? Should I add something else in
> the
> > mdp ?  In other words, how to be sure that the restraints are effectively
> > applied during the run ?
> >
> > I am using GROMACS 2018.2
> >
> > Thank in advance and happy new year to all
> >
> > St?phane
> > --
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>


--

Message: 2
Date: Thu, 10 Jan 2019 07:20:26 +0100
From: Mark Abraham 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] Dihedral restraints
Message-ID:

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

Hi,

You can see a working example at

https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log

so I conclude that your restraints are inactive, somehow. Please check your
include statements, etc.

Mark


On Wed., 9 Jan. 2019, 18:05 ABEL Stephane,  wrote:

> Thanks Mark for your reply
>
> In the log and edr files I only see an "Position Rest." term. So do you
> mean that the contributions on the dihedral restrains is added in in total
> energy without additional terms in the energy output in log file and the
> edr ?
>
> Thank you in advance for the clarification.
>
> St?phane
>
>
> --
>
> Message: 3
> Date: Wed, 9 Jan 2019 12:32:31 +0100
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: Re: [gmx-users] Dihedral restraints
> Message-ID:
>  xv8qbic+t1h1cwwcnkisdfxnoja7xbot...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> IIRC that's enough, for dihedral restraints. You will see energy
> contributions from the the restraints appear in your .log and .edr files if
> the restraints are active. I don't recall if there is anything printed by
> mdrun before the simulation commences.
>
> Mark
>
> On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane 
>

Re: [gmx-users] Dihedral restraints

[ABEL Stephane]

Thanks Mark for your reply 

In the log and edr files I only see an "Position Rest." term. So do you mean 
that the contributions on the dihedral restrains is added in in total energy 
without additional terms in the energy output in log file and the edr ?

Thank you in advance for the clarification. 

Stéphane


--

Message: 3
Date: Wed, 9 Jan 2019 12:32:31 +0100
From: Mark Abraham 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] Dihedral restraints
Message-ID:

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

Hi,

IIRC that's enough, for dihedral restraints. You will see energy
contributions from the the restraints appear in your .log and .edr files if
the restraints are active. I don't recall if there is anything printed by
mdrun before the simulation commences.

Mark

On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane  wrote:

> Hello
>
> I would like to apply some dihedral restraints in different residues of my
> protein during the production stage. For that I have added at the end of
> the protein itp the section
> [ dihedral_restraints ]. Is it enough ? Should I add something else in the
> mdp ?  In other words, how to be sure that the restraints are effectively
> applied during the run ?
>
> I am using GROMACS 2018.2
>
> Thank in advance and happy new year to all
>
> St?phane
> --
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[gmx-users] Dihedral restraints

[ABEL Stephane]

Hello 

I would like to apply some dihedral restraints in different residues of my 
protein during the production stage. For that I have added at the end of the 
protein itp the section 
[ dihedral_restraints ]. Is it enough ? Should I add something else in the mdp 
?  In other words, how to be sure that the restraints are effectively applied 
during the run ? 

I am using GROMACS 2018.2

Thank in advance and happy new year to all 

Stéphane
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[gmx-users] Why charge parameter of cations like Cu2+, Zn2+ in GROMOS 54a7 force field in GROMACS equals to zero?

[ABEL Stephane]

Hi 

All the the values in the charge column  in the ffnonbonded.itp are not used by 
GROMACS and remain present  for history reasons (and probably for compatibility 
with older GROMACS versions). The charges for each residue/molecules are now in 
the rtp. 

Best

Stéphane

--

Hi all,
I am trying to modify the original GROMOS 54a7 force field files implemented in 
GROMACS to add parameters of some new cations. But when I checked the 
ffnonbonded.itp, I found that the charge parameter of CU2+, Zn2+ equals to 
zero. Why? What does it mean? How GROMOS 54a7 force field calculate the 
electrostatic interaction? If I want to add some new ions, what should I do?
Thans in advance,
Chenlin

--

Chenlin Lu

Department of Chemical Engineering,

Tsinghua University, Beijing, 100084

Tel: 86-13120180517

Email: luc...@mails.tsinghua.edu.cn



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End of gromacs.org_gmx-users Digest, Vol 176, Issue 40
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Re: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

[ABEL Stephane]

Hello Justin, 

It is not clear to me it is bug. but I "think" that in these particular case 
densmap  does not truncate/rounds the data according to the bin value (i.e. 
0.05) I used in gmx densmap command line. To correct this I wrote a short 
script that change the x-y values like where the x/y values are proportional to 
the bin value : 

before :   

 /* x-axis:   0 0.054  3.95003 */ 

after 

 /* x-axis:   0 0.05  3.95 */ 

and then  I can obtain the ticks with gmx xpm2ps and the m2p. 

So by filling a redmine this problem will be reported and may be corrected  

Stéphane

--

Message: 2
Date: Wed, 7 Nov 2018 10:06:05 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Regarding xpm2ps with a xpm file obtained
from gmx densmap [update] and possible bug
Message-ID: 
Content-Type: text/plain; charset=iso-8859-2; format=flowed



On 11/5/18 1:19 PM, ABEL Stephane wrote:
> Hello again,
>
> Does the GROMACS team have some suggestions to help me to resolve my problem 
> with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in 
> the x/y axis (see below)? Since it seems a small bug should I fiil a redmine?

Is it actually a bug or do you just have extremely inconvenient data
that are difficult to assign convenient tick marks?

-Justin

> Thanks
>
> St?phane
>
>
>
> --
>
> Message: 2
> Date: Sun, 4 Nov 2018 13:19:06 +
> From: ABEL Stephane 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>  
> Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
>  gmx densmap [update] and possible bug
> Message-ID:
>  <3e39b768bb199548ab18f7289e7534af4887a...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="utf-8"
>
> Hi again,
>
> additional info about my issue with DensMap and xpm2ps
>
> I noticed that  the number of decimals of the x/y axis values ??in the xpm 
> are smaller may have an effect of presence of the minor and major ticks in 
> eps file obtained from xpm2ps (see below) Indeed with the same following 
> params in the m2p
>
> x-major  = 1.0
> x-minor  = 0.1
> x-firstmajor = 0.0
>
> y-major  = 1.0
> y-minor  = 0.1
> y-firstmajor = 0.0
>
> and different examples
>
> 1) With PDB as input and 1 frame  I obtained the following xpm with the 
> x-values (only a small part is shown) ---> minor and major ticlks are present 
> in the eps
> /* x-axis:  0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 
> 0.75 0.8 0.85 0.9 0.95 1 1.05 1.1 1.15 1.2 1.25 1.3 1.35 1.4 1.45 1.5 1.55 
> 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2 2.05 2.1 2.15 2.2 2.25 2.3 2.35 2.4 
> 2.45 2.5 2.55 2.6 2.65 2.7 2.75 2.8 2.85 2.9 2.95 3 3.05 3.1 3.15 3.2 3.25 
> 3.3 3.35 3.4 3.45 3.5 3.55 3.6 3.65 3.7 3.75 3.8 3.85 3.9 3.95 */
>
> 2) With PDB as input and 1000 frame I obtained the following xpm with the 
> x-values (only a small part is shown) ---> minor and major ticlks are NOT 
> present in the eps
> /* x-axis:  0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 
> 0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 
> 0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 
> 1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 
> 1.69958 1.74957 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 
> 2.14947 2.19945 2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 
> 2.59935 2.64934 2.69933 2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 
> 3.04924 3.09923 3.14922 3.1992 3.24919 3.29918 3.34917 3.39915 3.44914 
> 3.49913 3.54912 3.59911 3.64909 3.69908 3.74907 3.79906 3.84904 3.89903 
> 3.94902 */
>
> 3) With XTC as input and 1 frame I obtained the following xpm with the 
> x-values (only a small part is shown)  ---> minor and major ticlks are NOT 
> present in the eps
> /* x-axis:  0 0.054 0.11 0.150001 0.21 0.250002 0.32 0.350003 
> 0.43 0.450003 0.54 0.550004 0.64 0.650005 0.75 0.750005 
> 0.86 0.850006 0.97 0.950007 1.1 1.05001 1.10001 1.15001 1.20001 
> 1.25001 1.30001 1.35001 1.40001 1.45001 1.50001 1.55001 1.60001 1.65001 
> 1.70001 1.75001 1.80001 1.85001 1.90001 1.95001 2.1 2.05002 2.10002 
> 2.15002 2.20002 2.25002 2.30002 2.35002 2.40002 2.45002 2.50002 2.55002 
> 2.60002 2.65002 2.70002 2.75002 2.80002 2.85002 2.90002 2.95002 3.2 
> 3.05002 3.10002 3.15002 3.20002 3.25002 3.30002 3.35002 3.40002 3.45003 
> 3.50003 3.55003 3.60003 3.65003 3.70003 3.75003 3.80003 3.85003 3.90003 
> 3.95003 */
>
> and 4)  With XTC as

Re: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

[ABEL Stephane]

Hello again, 

Does the GROMACS team have some suggestions to help me to resolve my problem 
with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in 
the x/y axis (see below)? Since it seems a small bug should I fiil a redmine? 

Thanks 

Stéphane 



--

Message: 2
Date: Sun, 4 Nov 2018 13:19:06 +
From: ABEL Stephane 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
gmx densmap [update] and possible bug
Message-ID:
<3e39b768bb199548ab18f7289e7534af4887a...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="utf-8"

Hi again,

additional info about my issue with DensMap and xpm2ps

I noticed that  the number of decimals of the x/y axis values ??in the xpm are 
smaller may have an effect of presence of the minor and major ticks in eps file 
obtained from xpm2ps (see below) Indeed with the same following params in the 
m2p

x-major  = 1.0
x-minor  = 0.1
x-firstmajor = 0.0

y-major  = 1.0
y-minor  = 0.1
y-firstmajor = 0.0

and different examples

1) With PDB as input and 1 frame  I obtained the following xpm with the 
x-values (only a small part is shown) ---> minor and major ticlks are present 
in the eps
/* x-axis:  0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 
0.75 0.8 0.85 0.9 0.95 1 1.05 1.1 1.15 1.2 1.25 1.3 1.35 1.4 1.45 1.5 1.55 1.6 
1.65 1.7 1.75 1.8 1.85 1.9 1.95 2 2.05 2.1 2.15 2.2 2.25 2.3 2.35 2.4 2.45 2.5 
2.55 2.6 2.65 2.7 2.75 2.8 2.85 2.9 2.95 3 3.05 3.1 3.15 3.2 3.25 3.3 3.35 3.4 
3.45 3.5 3.55 3.6 3.65 3.7 3.75 3.8 3.85 3.9 3.95 */

2) With PDB as input and 1000 frame I obtained the following xpm with the 
x-values (only a small part is shown) ---> minor and major ticlks are NOT 
present in the eps
/* x-axis:  0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 
0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 
0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 
1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 
1.74957 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 
2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 
2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 
3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.59911 3.64909 3.69908 
3.74907 3.79906 3.84904 3.89903 3.94902 */

3) With XTC as input and 1 frame I obtained the following xpm with the x-values 
(only a small part is shown)  ---> minor and major ticlks are NOT present in 
the eps
/* x-axis:  0 0.054 0.11 0.150001 0.21 0.250002 0.32 0.350003 
0.43 0.450003 0.54 0.550004 0.64 0.650005 0.75 0.750005 
0.86 0.850006 0.97 0.950007 1.1 1.05001 1.10001 1.15001 1.20001 
1.25001 1.30001 1.35001 1.40001 1.45001 1.50001 1.55001 1.60001 1.65001 1.70001 
1.75001 1.80001 1.85001 1.90001 1.95001 2.1 2.05002 2.10002 2.15002 2.20002 
2.25002 2.30002 2.35002 2.40002 2.45002 2.50002 2.55002 2.60002 2.65002 2.70002 
2.75002 2.80002 2.85002 2.90002 2.95002 3.2 3.05002 3.10002 3.15002 3.20002 
3.25002 3.30002 3.35002 3.40002 3.45003 3.50003 3.55003 3.60003 3.65003 3.70003 
3.75003 3.80003 3.85003 3.90003 3.95003 */

and 4)  With XTC as input and 1000 frames I obtained the following xpm with the 
x-values (only a small part is shown)  ---> minor and major ticlks are NOT 
present in the eps
/* x-axis:  0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 
0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 
0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 
1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 
1.74956 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 
2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 
2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 
3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.5991 3.64909 3.69908 
3.74907 3.79906 3.84904 3.89903 3.94902 */


I used for the above examples the same densmap and xpm2ps commands show below 
and the 5.1.4 and 2018.2 gromacs version. It is a bug related to the rounding 
in the xpm2ps or I miss something ?

Thank you in advance for your help

St?phane


--

Message: 4
Date: Sat, 3 Nov 2018 17:45:53 +
From: ABEL Stephane 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
gmx densmap
Message-ID:
<3e39b768bb199548ab18f7289e7534af4887a...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="iso-8859-2"

Thanks you Justin f

[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

[ABEL Stephane]

Hi again, 

additional info about my issue with DensMap and xpm2ps

I noticed that  the number of decimals of the x/y axis values ​​in the xpm are 
smaller may have an effect of presence of the minor and major ticks in eps file 
obtained from xpm2ps (see below) Indeed with the same following params in the 
m2p 

x-major  = 1.0
x-minor  = 0.1
x-firstmajor = 0.0

y-major  = 1.0
y-minor  = 0.1
y-firstmajor = 0.0

and different examples

1) With PDB as input and 1 frame  I obtained the following xpm with the 
x-values (only a small part is shown) ---> minor and major ticlks are present 
in the eps
/* x-axis:  0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 
0.75 0.8 0.85 0.9 0.95 1 1.05 1.1 1.15 1.2 1.25 1.3 1.35 1.4 1.45 1.5 1.55 1.6 
1.65 1.7 1.75 1.8 1.85 1.9 1.95 2 2.05 2.1 2.15 2.2 2.25 2.3 2.35 2.4 2.45 2.5 
2.55 2.6 2.65 2.7 2.75 2.8 2.85 2.9 2.95 3 3.05 3.1 3.15 3.2 3.25 3.3 3.35 3.4 
3.45 3.5 3.55 3.6 3.65 3.7 3.75 3.8 3.85 3.9 3.95 */

2) With PDB as input and 1000 frame I obtained the following xpm with the 
x-values (only a small part is shown) ---> minor and major ticlks are NOT 
present in the eps
/* x-axis:  0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 
0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 
0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 
1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 
1.74957 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 
2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 
2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 
3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.59911 3.64909 3.69908 
3.74907 3.79906 3.84904 3.89903 3.94902 */

3) With XTC as input and 1 frame I obtained the following xpm with the x-values 
(only a small part is shown)  ---> minor and major ticlks are NOT present in 
the eps
/* x-axis:  0 0.054 0.11 0.150001 0.21 0.250002 0.32 0.350003 
0.43 0.450003 0.54 0.550004 0.64 0.650005 0.75 0.750005 
0.86 0.850006 0.97 0.950007 1.1 1.05001 1.10001 1.15001 1.20001 
1.25001 1.30001 1.35001 1.40001 1.45001 1.50001 1.55001 1.60001 1.65001 1.70001 
1.75001 1.80001 1.85001 1.90001 1.95001 2.1 2.05002 2.10002 2.15002 2.20002 
2.25002 2.30002 2.35002 2.40002 2.45002 2.50002 2.55002 2.60002 2.65002 2.70002 
2.75002 2.80002 2.85002 2.90002 2.95002 3.2 3.05002 3.10002 3.15002 3.20002 
3.25002 3.30002 3.35002 3.40002 3.45003 3.50003 3.55003 3.60003 3.65003 3.70003 
3.75003 3.80003 3.85003 3.90003 3.95003 */

and 4)  With XTC as input and 1000 frames I obtained the following xpm with the 
x-values (only a small part is shown)  ---> minor and major ticlks are NOT 
present in the eps
/* x-axis:  0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 
0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 
0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 
1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 
1.74956 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 
2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 
2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 
3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.5991 3.64909 3.69908 
3.74907 3.79906 3.84904 3.89903 3.94902 */


I used for the above examples the same densmap and xpm2ps commands show below 
and the 5.1.4 and 2018.2 gromacs version. It is a bug related to the rounding 
in the xpm2ps or I miss something ?

Thank you in advance for your help

Stéphane


--

Message: 4
Date: Sat, 3 Nov 2018 17:45:53 +0000
From: ABEL Stephane 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
gmx densmap
Message-ID:
<3e39b768bb199548ab18f7289e7534af4887a...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="iso-8859-2"

Thanks you Justin for your help but I still have the smae problem . I have 
changed in my m2p file the floowing fields

x-major  = 1.0; Major ticks on x axis every .. 
frames
x-minor  = 0.05 ; Id. Minor ticks
x-firstmajor = 0.0  ; First frame for major tick

y-major  = 1.0  ; Major ticks on y axis every .. frames
y-minor  = 0.05 ; Id. Minor ticks
y-firstmajor = 0.0

and use the xpm, some (not all) sticks  appeared in each axis but w/o the 
labels. I still do not understand why ...

St?phane


------

On 11/3/18 12:19 PM, ABEL Stephane wrote:
> Hello,
&g

[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap

[ABEL Stephane]

Thanks you Justin for your help but I still have the smae problem . I have 
changed in my m2p file the floowing fields

x-major  = 1.0; Major ticks on x axis every .. 
frames
x-minor  = 0.05 ; Id. Minor ticks
x-firstmajor = 0.0  ; First frame for major tick

y-major  = 1.0  ; Major ticks on y axis every .. frames
y-minor  = 0.05 ; Id. Minor ticks
y-firstmajor = 0.0

and use the xpm, some (not all) sticks  appeared in each axis but w/o the 
labels. I still do not understand why ...

Stéphane 


--

On 11/3/18 12:19 PM, ABEL Stephane wrote:
> Hello,
>
> I am using the below .m2p file as input for xpm2ps obtained from gmx densmap 
> (v2018.2), but I am not able to get axis range label. The commands I use for 
> densmap and xpm2ps
>
> gmx_mpi densmap -f MYXTC.xtc -s MYTPR.tpr -n  MYINDEX.ndx -b 15 -e 21 
> -bin 0.5  -aver z  -unit nm-2  -o  MYXPM.xpm
>
> gmx_mpi  xpm2ps -f MYXPM.xpm -di MYM2P.m2p -rainbow blue -gradient 0 0 0 -o 
> MYEPS.eps
>
> The range in the xpm for the x and y axis are 0 to 12.5097 (see below)
>
>  m2p -
>
> black  = no
> linewidth= 1
> titlefont= Helvetica
> titlefontsize= 20
> legend   = yes
> legendfont   = Helvetica
> legendlabel  =
> legend2label =
> legendfontsize   = 14
> xbox = 0
> ybox = 0
> matrixspacing= 20
> xoffset  = 0
> yoffset  = 0
> boxlinewidth = 1
> ticklinewidth= 1
> zerolinewidth= 1
> x-lineat0value   = none
> x-major  = 15.0

Here's your problem. You're telling xpm2ps to place major tick marks
every 15 units, but:

> /* x-axis:  0 0.0500388 0.100078 0.150116 0.200155 0.250194 0.300233 0.350271 
> 0.40031 0.450349 0.500388 0.550426 0.600465 0.650504 0.700543 0.750581 
> 0.80062 0.850659 0.900698 0.950736 1.00078 1.05081 1.10085 1.15089 1.20093 
> 1.25097 1.30101 1.35105 1.40109 1.45112 1.50116 1.5512 1.60124 1.65128 
> 1.70132 1.75136 1.8014 1.85143 1.90147 1.95151 2.00155 2.05159 2.10163 
> 2.15167 2.20171 2.25174 2.30178 2.35182 2.40186 2.4519 2.50194 2.55198 
> 2.60202 2.65205 2.70209 2.75213 2.80217 2.85221 2.90225 2.95229 3.00233 
> 3.05236 3.1024 3.15244 3.20248 3.25252 3.30256 3.3526 3.40264 3.45267 3.50271 
> 3.55275 3.60279 3.65283 3.70287 3.75291 3.80295 3.85298 3.90302 3.95306 */
> /* x-axis:  4.0031 4.05314 4.10318 4.15322 4.20326 4.25329 4.30333 4.35337 
> 4.40341 4.45345 4.50349 4.55353 4.60357 4.6536 4.70364 4.75368 4.80372 
> 4.85376 4.9038 4.95384 5.00388 5.05391 5.10395 5.15399 5.20403 5.25407 
> 5.30411 5.35415 5.40419 5.45422 5.50426 5.5543 5.60434 5.65438 5.70442 
> 5.75446 5.8045 5.85453 5.90457 5.95461 6.00465 6.05469 6.10473 6.15477 
> 6.20481 6.25484 6.30488 6.35492 6.40496 6.455 6.50504 6.55508 6.60512 6.65515 
> 6.70519 6.75523 6.80527 6.85531 6.90535 6.95539 7.00543 7.05546 7.1055 
> 7.15554 7.20558 7.25562 7.30566 7.3557 7.40574 7.45577 7.50581 7.55585 
> 7.60589 7.65593 7.70597 7.75601 7.80605 7.85608 7.90612 7.95616 */
> /* x-axis:  8.0062 8.05624 8.10628 8.15632 8.20636 8.25639 8.30643 8.35647 
> 8.40651 8.45655 8.50659 8.55663 8.60667 8.6567 8.70674 8.75678 8.80682 
> 8.85686 8.9069 8.95694 9.00698 9.05701 9.10705 9.15709 9.20713 9.25717 
> 9.30721 9.35725 9.40729 9.45732 9.50736 9.5574 9.60744 9.65748 9.70752 
> 9.75756 9.8076 9.85763 9.90767 9.95771 10.0078 10.0578 10.1078 10.1579 
> 10.2079 10.2579 10.308 10.358 10.4081 10.4581 10.5081 10.5582 10.6082 10.6583 
> 10.7083 10.7583 10.8084 10.8584 10.9084 10.9585 11.0085 11.0586 11.1086 
> 11.1586 11.2087 11.2587 11.3088 11.3588 11.4088 11.4589 11.5089 11.559 11.609 
> 11.659 11.7091 11.7591 11.8091 11.8592 11.9092 11.9593 */
> /* x-axis:  12.0093 12.0593 12.1094 12.1594 12.2095 12.2595 12.3095 12.3596 
> 12.4096 12.4597 12.5097 */

...your axis only goes to 12.5, so you get no labeling of any sort.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==



--

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[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap

[ABEL Stephane]

Hello, 

I am using the below .m2p file as input for xpm2ps obtained from gmx densmap 
(v2018.2), but I am not able to get axis range label. The commands I use for 
densmap and xpm2ps

gmx_mpi densmap -f MYXTC.xtc -s MYTPR.tpr -n  MYINDEX.ndx -b 15 -e 21 
-bin 0.5  -aver z  -unit nm-2  -o  MYXPM.xpm  

gmx_mpi  xpm2ps -f MYXPM.xpm -di MYM2P.m2p -rainbow blue -gradient 0 0 0 -o 
MYEPS.eps 

The range in the xpm for the x and y axis are 0 to 12.5097 (see below)

 m2p -

black  = no
linewidth= 1
titlefont= Helvetica
titlefontsize= 20
legend   = yes
legendfont   = Helvetica
legendlabel  =
legend2label =
legendfontsize   = 14
xbox = 0
ybox = 0
matrixspacing= 20
xoffset  = 0
yoffset  = 0
boxlinewidth = 1
ticklinewidth= 1
zerolinewidth= 1
x-lineat0value   = none
x-major  = 15.0
x-minor  = 0.1
x-firstmajor = 0.0
x-majorat0   = yes
x-majorticklen   = 8
x-minorticklen   = 4
x-label  = X (nm)
x-fontsize   = 16
x-font   = Helvetica
x-tickfontsize   = 12
x-tickfont   = Helvetica
y-lineat0value   = none
y-major  = 15.0
y-minor  = 0.5
y-firstmajor = 0.1
y-majorat0   = yes
y-majorticklen   = 8
y-minorticklen   = 4
y-label  = Y (nm)
y-fontsize   = 16
y-font   = Helvetica
y-tickfontsize   = 12
y-tickfont   = Helvetica

--- beginning of the xpm file 
/* legend:  "(nm^-2)" */
/* x-label: "x (nm)" */
/* y-label: "y (nm)" */
/* type:"Continuous" */
static char *gromacs_xpm[] = {
"250 250   51 1",
"A  c #FF " /* "0" */,
"B  c #FAFAFA " /* "7.34" */,
"C  c #F5F5F5 " /* "14.7" */,
"D  c #F0F0F0 " /* "22" */,
"E  c #EBEBEB " /* "29.4" */,
"F  c #E6E6E6 " /* "36.7" */,
"G  c #E0E0E0 " /* "44" */,
"H  c #DBDBDB " /* "51.4" */,
"I  c #D6D6D6 " /* "58.7" */,
"J  c #D1D1D1 " /* "66.1" */,
"K  c #CC " /* "73.4" */,
"L  c #C7C7C7 " /* "80.7" */,
"M  c #C2C2C2 " /* "88.1" */,
"N  c #BDBDBD " /* "95.4" */,
"O  c #B8B8B8 " /* "103" */,
"P  c #B3B3B3 " /* "110" */,
"Q  c #ADADAD " /* "117" */,
"R  c #A8A8A8 " /* "125" */,
"S  c #A3A3A3 " /* "132" */,
"T  c #9E9E9E " /* "139" */,
"U  c #99 " /* "147" */,
"V  c #949494 " /* "154" */,
"W  c #8F8F8F " /* "161" */,
"X  c #8A8A8A " /* "169" */,
"Y  c #858585 " /* "176" */,
"Z  c #808080 " /* "183" */,
"a  c #7A7A7A " /* "191" */,
"b  c #757575 " /* "198" */,
"c  c #707070 " /* "206" */,
"d  c #6B6B6B " /* "213" */,
"e  c #66 " /* "220" */,
"f  c #616161 " /* "228" */,
"g  c #5C5C5C " /* "235" */,
"h  c #575757 " /* "242" */,
"i  c #525252 " /* "250" */,
"j  c #4D4D4D " /* "257" */,
"k  c #474747 " /* "264" */,
"l  c #424242 " /* "272" */,
"m  c #3D3D3D " /* "279" */,
"n  c #383838 " /* "286" */,
"o  c #33 " /* "294" */,
"p  c #2E2E2E " /* "301" */,
"q  c #292929 " /* "308" */,
"r  c #242424 " /* "316" */,
"s  c #1F1F1F " /* "323" */,
"t  c #1A1A1A " /* "330" */,
"u  c #141414 " /* "338" */,
"v  c #0F0F0F " /* "345" */,
"w  c #0A0A0A " /* "352" */,
"x  c #050505 " /* "360" */,
"y  c #00 " /* "367" */,
/* x-axis:  0 0.0500388 0.100078 0.150116 0.200155 0.250194 0.300233 0.350271 
0.40031 0.450349 0.500388 0.550426 0.600465 0.650504 0.700543 0.750581 0.80062 
0.850659 0.900698 0.950736 1.00078 1.05081 1.10085 1.15089 1.20093 1.25097 
1.30101 1.35105 1.40109 1.45112 1.50116 1.5512 1.60124 1.65128 1.70132 1.75136 
1.8014 1.85143 1.90147 1.95151 2.00155 2.05159 2.10163 2.15167 2.20171 2.25174 
2.30178 2.35182 2.40186 2.4519 2.50194 2.55198 2.60202 2.65205 2.70209 2.75213 
2.80217 2.85221 2.90225 2.95229 3.00233 3.05236 3.1024 3.15244 3.20248 3.25252 
3.30256 3.3526 3.40264 3.45267 3.50271 3.55275 3.60279 3.65283 3.70287 3.75291 
3.80295 3.85298 3.90302 3.95306 */
/* x-axis:  4.0031 4.05314 4.10318 4.15322 4.20326 4.25329 4.30333 4.35337 
4.40341 4.45345 4.50349 4.55353 4.60357 4.6536 4.70364 4.75368 4.80372 4.85376 
4.9038 4.95384 5.00388 5.05391 5.10395 5.15399 5.20403 5.25407 5.30411 5.35415 
5.40419 5.45422 5.50426 5.5543 5.60434 5.65438 5.70442 5.75446 5.8045 5.85453 
5.90457 5.95461 6.00465 6.05469 6.10473 6.15477 6.20481 6.25484 6.30488 6.35492 
6.40496 6.455 6.50504 6.55508 6.60512 6.65515 6.70519 6.75523 6.80527 6.85531 
6.90535 6.95539 7.00543 7.05546 7.1055 7.15554 7.20558 7.25562 7.30566 7.3557 
7.40574 7.45577 7.50581 7.55585 7.60589 7.65593 7.70597 7.75601 7.80605 7.85608 
7.90612 7.95616 */
/* x-axis:  8.0062 8.05624 8.10628 8.15632 8.20636 8.25639 8.30643 8.35647 
8.40651 8.45655 8.50659 8.55663 8.60667 8.6567 8.70674 8.75678 8.80682 8.85686 
8.9069 8.95694 9.00698 9.05701 9.10705 9.15709 9.20713 9.25717 9.30721 9.35725 

[gmx-users] pcoupltype

[ABEL Stephane]

Just my 2 cents

If I recall well CHARMM36 and others force fields (such as lipid14) were 
initially parametrized and validated using the anisotropic pressure
 coupling scheme. So it make sense to use it instead of semi-isotropic pressure 
coupling. Moreover I found that if the membrane system is  well equilibrated 
(for instance > 100 ns of NPT is semiisotropic for POPC or DOPC membranes), you 
can switch safely to anistropic pressure scheme and does not observe 
significant deformations of the bilayer. These observations are based on my 
simulations and are of course not general?  

Stéphane

--

Message: 4
Date: Wed, 31 Oct 2018 15:03:55 +
From: "Gonzalez Fernandez, Cristina" 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] pcoupltype
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"

Thank you very much Kevin and Justin for your information

-Mensaje original-
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Justin 
Lemkul
Enviado el: mi?rcoles, 31 de octubre de 2018 13:53
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] pcoupltype



On 10/30/18 3:42 PM, Kevin Boyd wrote:
> Hi,
>
> For membrane systems you typically want to use semi-isotropic pressure
> coupling. If instead you want to simulate *one* lipid (as a ligand)
> with a protein in solution, you should stick to isotropic pressure
> coupling. I've never heard of any anisotropic pressure coupling
> protocols in equilibrium NPT systems like what you describe.

Indeed, anisotropic coupling is best applied to solids/crystals. In the case of 
membranes, anisotropic coupling leads to deformation of the box over long 
periods of time.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Message: 5
Date: Wed, 31 Oct 2018 16:06:22 +0100
From: Ramon Guix? 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs+CHARMM36+GPUs induces
protein-membranesystem collapse?
Message-ID:

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

Ok, I mean, It makes sense what you say.
I still I don't understand though how this has not been spotted before, I
mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I
have replicated the problem using versions 5, 2016, and 2018...? I know I
sound a little desperate, but is there any workaround I could use to
proceed until this is resolved?
Ramon

On Wed, Oct 31, 2018 at 3:51 PM Justin Lemkul  wrote:

>
>
> On 10/31/18 10:47 AM, Ramon Guix? wrote:
> > Hi Justin,
> >
> > I do not have access to GPUs with ECC, but I have actually run the same
> tpr
> > in different machines with different GPUs, including GTX 980, 1060 and
> > 1080. In all cases, I get the same problem. Although they are all
> non-ECC
> > cards, it is quite unlikely that a bit flip is behind this, isn't it?
>
> Certainly is. It wasn't clear if you were just running over and over
> again on the same card or what.
>
> > In fact, I had simulated before CHARMM-GUI systems using GTX cards and
> > never had a problem. Since this has only benn happening recently to me,
> so
> > I am wondering if I should blame the new force field (CHARMM36m) or
> whether
> > CHARMM-GUI changed something in the way they generate gromacs topologies?
>
> I sincerely doubt it's the force field. We validate that extensively
> across many compounds to verify that GROMACS and CHARMM compute the
> forces the same (I do this myself when we produce a new force field
> port). We don't (can't) do that easily on GPU, but if the forces are
> different, that points to a software bug, because everything about the
> CPU implementations is identical. Given that you have a sudden change in
> system behavior, that further points to a software bug, in my opinion,
> because if something was fundamentally wrong with the force field, (1)
> you would see it on CPU runs and (2) it would almost certainly occur
> much earlier in the simulation.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> 

[gmx-users] xpm2ps (2018.3) does print axis labels

[ABEL Stephane]

Sorry for the double post, I resend my message (below) since I have received no 
response from you guys 


Hello,

I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated 
with gmx_mpi densmap. For example If I use  the following xpm (1) and m2p (2) 
files and the following command the x and y labels are not plotted in the eps 
figure.. The xpm seems OK for me. It is a bug

mx_mpi xpm2ps -f MY_2DXY_DensMap.xpm -rainbow blue -gradient 1 1 1 -aver z -di  
2D_DensityMap_params.m2p -o MY_2DXY_DensMap -xpm test.xpm

You can download the xpm and m2p here for testing

1) 
https://drive.google.com/file/d/1LI5Y2-OCYyQS2FImRK9Axhcu-TLBQ9gg/view?usp=sharing
2) 
https://drive.google.com/file/d/1ETZtBAqrcn17SJHB6aKPYI-lWOdAF9Sp/view?usp=sharing

Can you help me ? 

Thank you in advance

Stéphane
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Re: [gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

[ABEL Stephane]

Thank you very much Dallas, it worked. 

Stéphane


--

Haven't tried it, but seems to me you generate a .tpr file with the
protein orientated correctly within the box, then use trjconv -fit

Catch ya,

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

On Wed, 24 Oct 2018 at 20:38, ABEL Stephane  wrote:
>
> Hello All,
>
> I have  basic questions regarding the procedure to generate an new xtc where 
> a membrane protein inserted a detergent micelle is properly oriented for the 
> computation of 2D density Map. Indeed for this calculation I need to have the 
> protein-surfactant complex properly oriented along a given axis (say Z). For 
> this I chose two atoms and define a vector in my protein and I would like 
> that this vector // to z axis. How to this in GROMACS? I think that editconf 
> can do the trick, however I notice that this tool cannot use and output an 
> xtc file. So is there an alternative approach ? If yes how (an example of 
> command line will be very useful)
>
> Thanks in advance
>
> Stephane
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[gmx-users] xpm2ps (2018.3) does print axis labels

[ABEL Stephane]

Hello, 

I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated 
with gmx_mpi densmap. For example If I use  the following xpm (1) and m2p (2) 
files and the following command the x and y labels are not plotted in the eps 
figure. Same behavior problem occurs if I did not a m2p file. The xpm OK for 
me. 

mx_mpi xpm2ps -f MY_2DXY_DensMap.xpm -rainbow blue -gradient 1 1 1 -aver z -di  
2D_DensityMap_params.m2p -o MY_2DXY_DensMap -xpm test.xpm

You can download the xpm and m2p here 

1) 
https://drive.google.com/file/d/1ETZtBAqrcn17SJHB6aKPYI-lWOdAF9Sp/view?usp=sharing
2) 
https://drive.google.com/file/d/1LI5Y2-OCYyQS2FImRK9Axhcu-TLBQ9gg/view?usp=sharing

Can you help me ? Thank you 

Stéphane
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[gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

[ABEL Stephane]

Hello All, 

I have  basic questions regarding the procedure to generate an new xtc where a 
membrane protein inserted a detergent micelle is properly oriented for the 
computation of 2D density Map. Indeed for this calculation I need to have the 
protein-surfactant complex properly oriented along a given axis (say Z). For 
this I chose two atoms and define a vector in my protein and I would like that 
this vector // to z axis. How to this in GROMACS? I think that editconf can do 
the trick, however I notice that this tool cannot use and output an xtc file. 
So is there an alternative approach ? If yes how (an example of command line 
will be very useful) 

Thanks in advance

Stephane
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[gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

[ABEL Stephane]

Dear all, 

I would like to obtain a 2D density map plot as for instance Fig. 4 in the 
following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein inserted 
in a surfactant micelle with gmx densmap and xpm2ps .  I have few questions 

- Have any of you ever done this type of plot? If yes, how? 
- What parameters for densmap and/or xpm2ps did you use? 
- How did you combine the protein and surfactant xpm files into a single one to 
obtain the same plot as Fig. 4

Thanks in advance for your help 

Stéphane
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Re: [gmx-users] g_mindist error "Cannot open file with NULL filename string"

[ABEL Stephane]

Hello Mark,

Thank you for your response, I have also tested the same command line* with 
different GMX versions (see below); 

* gmx_mpi mindist -f /ccc/store/cont003/XXX////XTC/myXTC.xtc -s 
MYPDB.pdb -n Hydratation_Protein_OGNG.ndx -b 20 -e 215000 -dt 4 -d 0.4 
-respertime -printresname -group -od 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg -on 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg

With GMX467 ---> OK 


With GMX5.1.4 (segmentation fault) --

Group 0 (Protein_HeavyAtoms) has  4976 elements
Group 1 (OGNG_AlkylChain) has  1530 elements
Group 2 ( OGNG_Headgroup) has  2244 elements
Group 3 (OGNG_All_HeavyAtoms) has  3774 elements
Group 4 (   Water_oxygen) has 6 elements
Select a group: Select a group: ^MReading frame   0 time0.000   
^MReading frame   0 time 20.000
Back Off! I just backed up 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to 
./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.2#

Back Off! I just backed up 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to 
./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.2#
[irene1022:52095:0] Caught signal 11 (Segmentation fault)
 backtrace 
 2 0x00068d1c mxm_handle_error()  
/var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641
 3 0x0006926c mxm_error_signal_handler()  
/var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616
 4 0x00035270 killpg()  ??:0
 5 0x000471ad _IO_vfprintf_internal()  :0
 6 0x00051827 __GI_fprintf()  :0
 7 0x003b3cd8 xvgr_header()  ??:0
 8 0x003b3c70 xvgropen_type()  ??:0
 9 0x00545400 dist_plot.a()  gmx_mindist.c:0
10 0x00543990 gmx_mindist()  ??:0
11 0x001e1ff3 _ZN3gmx24Comman

With GMX2018 and 2018.2 (fatal error) --

Group 0 (Protein_HeavyAtoms) has  4976 elements
Group 1 (OGNG_AlkylChain) has  1530 elements
Group 2 ( OGNG_Headgroup) has  2244 elements
Group 3 (OGNG_All_HeavyAtoms) has  3774 elements
Group 4 (   Water_oxygen) has 6 elements
Select a group: Select a group: ^MReading frame   0 time0.000   
^MReading frame   0 time 20.000
Back Off! I just backed up 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to 
./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.1#

Back Off! I just backed up 
3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to 
./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.1#

---
Program: gmx mindist, version 2018
Source file: src/gromacs/fileio/gmxfio.cpp (line 345)

Fatal error:
Cannot open file with NULL filename string

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
+ echo 0 2
+ echo 0 3
+ echo 0 4
+ exit 0

Please note that if I remove the "-group" and "-printresname" arguments the 
program also crashes, execpt with GMX467.

I will fill a redmine issue

HTH

Stéphane


--

Message: 5
Date: Tue, 25 Sep 2018 22:23:42 +0200
From: Mark Abraham 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] g_mindist error "Cannot open file with NULL
filename string"
Message-ID:

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

Hi,

That looks like some kind of bug in mindist. Does an earlier version work
for you? Are you able to upload a report for us at
https://redmine.gromacs.org?

Thanks

Mark

On Tue, Sep 25, 2018 at 3:30 PM ABEL Stephane  wrote:

> Hi All,
>
> I would like to use g_mindist (vGMX2018.2) to compute the number of total
> contacts between each residue of a protein and surfactant molecules. For
> this I use the following command
>
>  gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 20 -e
> 215000 -dt 4 -d 0.4 -respertime -printresname -group -od
> Protein_AlkylChain_Contact_min_res.xvg -on
> Protein_AlkylChain_Contact_Number.xvg < Protein_AlkylChain.txt
>
>
>  I obtain the following fatal error, Why ?
>
>  ---
> Program: gmx mindist, version 2018.2
> Source file: src/gromacs/fileio/gmxfio.cpp (line 345)
>
> Fatal error:
> Cannot open file with NULL filename string
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Please note I al

[gmx-users] g_mindist error "Cannot open file with NULL filename string"

[ABEL Stephane]

Hi All,

I would like to use g_mindist (vGMX2018.2) to compute the number of total 
contacts between each residue of a protein and surfactant molecules. For this I 
use the following command

 gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 20 -e 215000 -dt 
4 -d 0.4 -respertime -printresname -group -od  
Protein_AlkylChain_Contact_min_res.xvg -on 
Protein_AlkylChain_Contact_Number.xvg < Protein_AlkylChain.txt


 I obtain the following fatal error, Why ?

 ---
Program: gmx mindist, version 2018.2
Source file: src/gromacs/fileio/gmxfio.cpp (line 345)

Fatal error:
Cannot open file with NULL filename string

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

Please note I also would like that each contact between each residue and 
surfactant atoms is counted as one. Is this possible with the command above ?

Thanks for you help,

Stéphane

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[gmx-users] minimization is not converging (Bratin Kumar Das)

[ABEL Stephane]

>> getting failed for my system

Not clear to me. What are the errors? Did you passed all the steps. CHARMM-ui 
is quite robust. So if the initial structure of the protein and the pdb 
correctly formated and complete, CHARMM-GUI should work. 

Stéphane

-
Dear ABEL,
   I tried CHARMM-gui but the charmm gui is getting failed
for my system.


On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane  wrote:

> Hi
>
> Did you try to use CHARMM-gui and use the gromacs files generated for this
> system to see if your problem is resolved?
>
> St?phane
>
> --
>
> Message: 5
> Date: Thu, 6 Sep 2018 19:55:07 +0530
> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] minimization is not converging
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you sir
>
> On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul  wrote:
>
> >
> >
> > On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > > Respected Dr. Justin
> > >   To avoid the complicacy I
> solvated
> > > only the protein pdb in a pbc box and tried for minimizatin. There also
> > > minimization is not converging. Sir, till now I learned to carry out
> > > protein ligand system md simulation successfully. I tried all possible
> > ways
> > > to simulate the my membrane protein system. I failed. Is it possible
> that
> > > the PDB file itself have some serious issue with its coordinates. the
> > > structure refinement is required may be.
> >
> > It may, and I have already suggested a few things for you to check.
> > Please do so.
> >
> > If you can provide more specific diagnostics of what is happening,
> > someone on this list might be able to suggest something. What you've
> > provided thus far is a generic instability that no one can diagnose.
> > Investigate the structure, check for pdb2gmx warnings, follow the
> > diagnostics I've already suggested, and report back with specific
> > observations, a PDB code, and exact errors or warnings you get from any
> > program if you need further help.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> --
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
> End of gromacs.org_gmx-users Digest, Vol 173, Issue 17
> **
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--

Message: 4
Date: Thu, 6 Sep 2018 22:42:01 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] minimization is not converging (Bratin Kumar
Das)
Message-ID:

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

Dear ABEL,
   I tried CHARMM-gui but the charmm gui is getting failed
for my system.


On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane  wro

Re: [gmx-users] minimization is not converging (Bratin Kumar Das)

[ABEL Stephane]

Hi

Did you try to use CHARMM-gui and use the gromacs files generated for this 
system to see if your problem is resolved? 

Stéphane

--

Message: 5
Date: Thu, 6 Sep 2018 19:55:07 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] minimization is not converging
Message-ID:

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

Thank you sir

On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul  wrote:

>
>
> On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > Respected Dr. Justin
> >   To avoid the complicacy I solvated
> > only the protein pdb in a pbc box and tried for minimizatin. There also
> > minimization is not converging. Sir, till now I learned to carry out
> > protein ligand system md simulation successfully. I tried all possible
> ways
> > to simulate the my membrane protein system. I failed. Is it possible that
> > the PDB file itself have some serious issue with its coordinates. the
> > structure refinement is required may be.
>
> It may, and I have already suggested a few things for you to check.
> Please do so.
>
> If you can provide more specific diagnostics of what is happening,
> someone on this list might be able to suggest something. What you've
> provided thus far is a generic instability that no one can diagnose.
> Investigate the structure, check for pdb2gmx warnings, follow the
> diagnostics I've already suggested, and report back with specific
> observations, a PDB code, and exact errors or warnings you get from any
> program if you need further help.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


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[gmx-users] Use different version of tpr in the same simulation... possible ?

[ABEL Stephane]

Hi there

For different reason, I have to use a different version  of GROMACS (GMX2016.4) 
to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an  
error appears about the tpr "reading tpx file  version 112 with version 110 
program" Is there an alternative to do what I want ?  

Thank you 
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 57

[ABEL Stephane]

Thank you Shreyas, Pedro and Mark Abraham for forwarding my initial message to 
the program's author who responded to me

Stéphane  

--

--

Message: 3
Date: Sat, 16 Jun 2018 19:45:28 +0200
From: Shreyas Kaptan 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] About the "g_contacts" program for gromacs
Message-ID:

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

In the paper it mentions that:

This paper and its associated computer program are available via the
Computer Physics Communication homepage on ScienceDirect (
http://www.sciencedirect.com/science/journal/00104655).

Hope that helps.

On Thu, Jun 14, 2018 at 5:53 PM ABEL Stephane  wrote:

> Hi there,
>
> Do you know where I can find the program g_contacts developed by Christian
> Blau & Helmut Grubmuller and described in the following paper "g_contacts:
> Fast contact search in bio-molecular ensemble data. Computer Physics
> Communications
> Volume 184, Issue 12, December 2013, Pages 2856-2859"
> https://www.sciencedirect.com/science/article/pii/S0010465513002464. I
> would like to test it. In addition, does this tool work with the  5.1.X or
> newer versions of gromacs. (It was initially developed for gromacs 4.6) .
>
> Thanks
>
> A bient?t
>
> St?phane
>
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>


--
Shreyas Sanjay Kaptan


--

Message: 4
Date: Sat, 16 Jun 2018 19:04:39 +0100
From: Pedro Deira 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] About the "g_contacts" program for gromacs
Message-ID:

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

I never managed to get it working with 5.x, I have a separate 4.x
installation to run g_contacts.

p.

On Thu, 14 Jun 2018, 16:53 ABEL Stephane,  wrote:

> Hi there,
>
> Do you know where I can find the program g_contacts developed by Christian
> Blau & Helmut Grubmuller and described in the following paper "g_contacts:
> Fast contact search in bio-molecular ensemble data. Computer Physics
> Communications
> Volume 184, Issue 12, December 2013, Pages 2856-2859"
> https://www.sciencedirect.com/science/article/pii/S0010465513002464. I
> would like to test it. In addition, does this tool work with the  5.1.X or
> newer versions of gromacs. (It was initially developed for gromacs 4.6) .
>
> Thanks
>
> A bient?t
>
> St?phane
>
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[gmx-users] About the "g_contacts" program for gromacs

[ABEL Stephane]

Hi there,

Do you know where I can find the program g_contacts developed by Christian Blau 
& Helmut Grubmuller and described in the following paper "g_contacts: Fast 
contact search in bio-molecular ensemble data. Computer Physics Communications
Volume 184, Issue 12, December 2013, Pages 2856-2859" 
https://www.sciencedirect.com/science/article/pii/S0010465513002464. I would 
like to test it. In addition, does this tool work with the  5.1.X or newer 
versions of gromacs. (It was initially developed for gromacs 4.6) .

Thanks 

A bientôt

Stéphane

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[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[ABEL Stephane]

I know the paper but the webpage

Thanks you Viveca 

--

Message: 2
Date: Fri, 6 Apr 2018 16:45:45 +0200
From: Viveca Lindahl 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] Speed up simulations with GROMACS with
virtual interaction sites
Message-ID:

[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[ABEL Stephane]

Many thanks Anthony

I will read your post blog. I have another quick question: Does the approach 
work by defaults (w/o modifications) for other biomolecules such as surfactants 
or it is necessary to construct a virtual site table as we can found for 
protein in the charmm*.ff distribution ? 

Stéphane



--

Message: 3
Date: Fri, 6 Apr 2018 09:33:46 +
From: Anthony Nash <anthony.n...@dpag.ox.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
virtual interaction sites
Message-ID:
<84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I tried something like this about a year ago and I put an instructional blog 
post together. Warning: it was pulled together from a paper I found and not my 
own efforts although I did get it to work. Any questions I might not be able to 
respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Hi gmx users,

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

St?phane

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[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[ABEL Stephane]

Hi gmx users, 

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

Stéphane 

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[gmx-users] Possible to extract gro file from a tpr?

[ABEL Stephane]

Hi 

A quick question here, before to read this response I thought (but never 
tested) that it was possible to extract a pdb from a tpr since we use one to 
generate a tpr with grompp. So how is store the atomic coordinates of a system 
in a tpr file ?

Thanks  

--

Message: 1
Date: Tue, 3 Apr 2018 10:54:09 +0200
From: Viveca Lindahl 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Possible to extract gro file from a tpr?
Message-ID:

[gmx-users] Simulation of D-Alanine (prasun kumar)

[ABEL Stephane]

Hi 

I added the same problems few days ago.There is no hdb entries for D-AA, so 
GROMACS can not generate the missing Hs. So I would suggest you to use 
CHARMM-GUI, instead and use a fake *.itp with the L-ALA (ALA) renamed to DALA. 

Good luck

Stéphane 

--

Hi Group:

I am trying to simulate a peptide containing D-Alanine (DAL). For this
purpose, I am using Charmm36m Force Field.
While running the command 'pdb2gmx -f input.pdb -ignh -ff charmm36-july17',
I got an error saying 'DAL is not defined' (something similar to this). I
understand that the residue name DAL is not given in the merged.rtp file.
However, DALA is present. Keeping the nomenclature in mind, I added a line
"DAL   DALA" in merged.r2b file. Now my command is running, but  it is
not able to add hydrogen atoms to DAL residues.

Please guide me.

Thank You in advance
Prasun

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success


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Re: [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

[ABEL Stephane]

OK thank you Justin for the confirmation

Stéphane

--

On 3/9/18 6:55 AM, ABEL Stephane wrote:
> Dear all,
>
> I am constructing a top file for gramicidin A a short that contains a 
> succession of D- and L-AAs (the exact sequence is 
> HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH)
>  and have a unexpected problem whenI use  charmm36 . Indeed it seems that a 
> dihedral parameter is missing in the last charmm36m release for GROMACS but 
> also (?) in the original last CHARMM toppar file (including CHARMM36m). For 
> instance for linking the (D-LEU --> L-TRP) I need the CTD1  C  NH1 CT1 (where 
> the CTD1 is the carbon atom type for D-LEU) however I did not find this 
> parameters in the CHARMM36.
>
> Am I missing something or did something wrong ?? It is valid to use the 
> values of CTD1  C  NH1 CT1.

Yes. The CTD1 atom type is just a clone of CT1, and the parameters for
CT1-C-NH1-CTD1 are copied from CT1-C-NH1-CT1, so the parameters for
CTD1-C-NH1-CT1 will also be the same as CT1-C-NH1-CT1. I'm not sure why
that's never caused a problem before, but I'll get it fixed in both
CHARMM and GROMACS.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


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[gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

[ABEL Stephane]

Dear all, 

I am constructing a top file for gramicidin A a short that contains a 
succession of D- and L-AAs (the exact sequence is 
HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH)
 and have a unexpected problem whenI use  charmm36 . Indeed it seems that a 
dihedral parameter is missing in the last charmm36m release for GROMACS but 
also (?) in the original last CHARMM toppar file (including CHARMM36m). For 
instance for linking the (D-LEU --> L-TRP) I need the CTD1  C  NH1 CT1 (where 
the CTD1 is the carbon atom type for D-LEU) however I did not find this 
parameters in the CHARMM36. 

Am I missing something or did something wrong ?? It is valid to use the values 
of CTD1  C  NH1 CT1.

Thanks in advance 

Stéphane

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Re: [gmx-users] CMAP entries for D-residues with GROMACS (Justin Lemkul)

[ABEL Stephane]

OK I see thank you, Justin

Bye

On 3/2/18 10:50 AM, ABEL Stephane wrote:
> Dear all,
>
> I am interested to simulate a system with gramicidin A  that contains D-AAs 
> (D-LEU and D-VaL)  and I am wondering if the CMAP entries in the cmap.itp 
> file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this 
> because I see that the CHARMM force field library contains a file 
> (toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be 
> redefined.

The parameters are not "redefined," they are given for the D-amino
acids, which have a different C-alpha type (CTD1 instead of CT1). The
latest CHARMM36 port supports D-amino acids, with the exception of the
.hdb file, which does not have entries for them.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] CMAP entries for D-residues with GROMACS

[ABEL Stephane]

Dear all, 

I am interested to simulate a system with gramicidin A  that contains D-AAs 
(D-LEU and D-VaL)  and I am wondering if the CMAP entries in the cmap.itp file 
(charmm36-jul2017.ff) are used for these types of AA ? I am asking this because 
I see that the CHARMM force field library contains a file 
(toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be 
redefined.

Thank you for you response. 

Stéphane
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[gmx-users] disulfide bond missing even with -ss

[ABEL Stephane]

Hi, 

If your are not sure that SS is formed or taken into account in the top file,. 
You could do a short minimization of the initial structure and observe  the 
minimized structure has the SS bond. If it also a good way to see if the top 
file is correct. 

Sté


De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
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gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
[gromacs.org_gmx-users-requ...@maillist.sys.kth.se]
Envoyé : dimanche 21 janvier 2018 17:48
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Today's Topics:

   1. Re: disulfide bond missing even with -ss (MD)
   2. Re: disulfide bond missing even with -ss (Justin Lemkul)


--

Message: 1
Date: Sun, 21 Jan 2018 11:42:23 -0500
From: MD 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] disulfide bond missing even with -ss
Message-ID:

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

On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 11:30 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:
>>
>>
>>> On 1/21/18 11:20 AM, MD wrote:
>>>
>>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:


 On 1/21/18 10:59 AM, MD wrote:
>
> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul 
> wrote:
>
>>
>> On 1/21/18 10:46 AM, MD wrote:
>>
>>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
>>> wrote:
>>>
>>> On 1/21/18 10:29 AM, MD wrote:

 I modified the specbond.dat and change the cutoff to be 2.04A, still
>
> nothing...
>
>> Please don't spam the list with minute-by-minute updates.
>>
>> ?
>>
> sorry
>
 ?for the scattered information, ?
 I didn't mean to spam the thread..



 Provide your pdb2gmx command, full screen output, and whatever
 evidence

 you have that the bond wasn't formed. The definitive answer is in
 your

> topology. If it's not there, we can diagnose.
>
> ?
>
> command line: gmx pdb2gmx -f ncat.pdb -o ncat.gro -water spc -ignh
>
 -ss



 Link CYS-335 SG-2487 and CYS-338 SG-2507 (y/n) ?y

 There is no indication that anything went wrong, and this should
 have

 been
>>> done. Are you saying that there is no line in the topology
>>> specifying a
>>> bond between atoms 2487 and 2507?
>>>
>>> ?Right. I didn't see anything said about the bond. I went forward to
>>>
>> the
>> step of em.mdp and got a minimized gro, which was converted to pdb.
>> And
>> I
>> found no disulfide bond in the pdb file.?
>>
>> So, to be clear, please answer these two questions directly:
>>
> 1. You find no line in [bonds] in topol_Protein_chain_B.itp file
> between
> atoms 2487 and 2507?
>
> ?Correct.?
>


 2. When you visualize the structure, both Cys335 and Cys338 are in their

> thiol (-SH) form?
>
> T
 ?hey are not in thiol form. ?
 ?
 https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_
 EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
 ?

 This is not consistent with your above assertion. If your structure,
>>> after
>>> pdb2gmx or any point thereafter, does not have -SH, then you are
>>> modeling a
>>> disulfide. You can't simultaneously have no bond defined in the topology
>>> and also have no thiols. These are mutually exclusive. I suspect the bond
>>> was formed and you're perhaps looking in the wrong place.
>>>
>>
>> ?Then how can we explain there are no bond formed in the
>> topol_Protein_chain_B.itp??
>>
>
> Is the image you showed before or after pdb2gmx? I'm trying to help you
> figure this out, but the information at hand is not consistent unless this
> structure is pre-pdb2gmx. What I was asking about was a structure *after*
> processing with 

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

[ABEL Stephane]

>> Would you be willing to share the exact sequence of events, commands, etc. 
>> that worked?

OK, 

Consider that the Atosiban cyclic peptide 
(https://fr.wikipedia.org/wiki/Atosiban) with 2 custom residues 
(3-Mercaptopropionyl, MEr) and ethyloxyde TYR (TYO) at Nter. The Mer is bonded 
to the CYS with SS bond and to TYO. Since we have no hdb for  for these 
residues. I first added manually the Hs in MEr and TYO with pymol with their 
corresponding names listed in the rtp (myAtosiban.pdb). 

My "problem" was to linked the Mer and TYO  and TYO with ILE by two peptide 
bonds and thus form a SS bond with Mer and CYS

1) consider the Mer and TYO as Protein residues and add  in residuetypes.dat 
the following lines

 MER Protein
 TYO Protein
 
 2) construct the corresponding rtp for these two custom residues (the RESP 
charges were derived with PyRED) Disclaimer ; these charges are "absolutely 
not" tested 
 
  TYO rtp 
  ; RESP partial charges derived from PyRED
  ; residue has similar structure than TYR
[ TYO ]
 [ atoms ]
 NN-0.5197 1
 HH 0.2770 2
CACX0.4385 3
HAH10.0423 4
CBCT   -0.1978 5
   HB1HC0.0698 6
   HB2HC0.0698 7
CGCA0.0563 8
   CD1CA   -0.2130 9
   HD1HA0.141710
   CE1CA   -0.162711
   HE1HA0.137312
   CZ C 0.271413
   OE OS   -0.384414
   C2 CT0.171515
   H21H10.031316
   H22H10.031317
   C3 CT   -0.052618
   H31HC0.019419
   H32HC0.019420
   H33HC0.019421
   CD2CA   -0.213022
   HD2HA0.141723
   CE2CA   -0.162724
   HE2HA0.137325
C C 0.404726 ; CO in PyRED
O O-0.574227

[ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   CD1
CG   CD2
   CD1   HD1
   CD1   CE1
   CE1   HE1
   CE1CZ
CZOE
OEC2
C2H21
C2H22
C2C3
C3H31
C3H32
C3H33
CZCE2
   CE2   HE2
   CE2   CD2
   CD2   HD2
 C O
 C+N  ---> here the trick to make a peptide bond with ILE

 [ impropers ]
-CCA N H
CA+N C O
CG   CE2   CD2   HD2
CZ   CD2   CE2   HE2
   CD1CZ   CE1   HE1
CG   CE1   CD1   HD1
   CD1   CD2CGCB
   CE1   CE2CZOE
   
 MER 
 
 ; Mercapto
;
;  S1
;   |
;  H21-C2-H22
;   |
;   H31-C3-H32
;   |
;   C=O

; RESP partial charges derived from PyRED

[ MER ]
 [ atoms ]
S1  S -0.1994  1
C2  CT 0.0424  2   ; same as C3 in PyRED
H21 H1 0.0631  3   ; same as H31 in PyRED
H22 H1 0.0631  4   ; same as H32 in PyRED
C3  CT-0.0157  5   ; same as C4 in PyRED
H31 H1 0.0295  6   ; same as H41 in PyRED
H32 H1 0.0295  7   ; same as H42 in PyRED
C   C  0.5373  8   ; same as C2 in PyRED
O   O -0.5498  9   ; same as O1 in PyRED

[ bonds ]
 S1   C2
 C2   H21
 C2   H22
 C2   C3
 C3   H31
 C3   H32
 C3   C
 CO
 C   +N  --> here the trick to make a peptide bond with TYO

 [ impropers ]
C3+N C O

3) to make a SS bond between Mer and CYS. Add in the specbondat the following 
line 

1
MER S1  1   CYX SG  1   0.20380 MER  CYX  ;; S-S 
bond distance in Amber

And to finish use the following command to construct the top file 

mpirun -np 1 gmx_mpi pdb2gmx -f myAtosiban.pdb -p myAtosiban.top -o 
myAtosiban_H.pdb -i myAtosiban_posre.itp -missing -rtpres

and perform a short minimization to check if the three bonds are correctly set 
(not broken). 

Stéphane 

--

Message: 2
Date: Mon, 15 Jan 2018 12:42:16 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff -- Resolved
Message-ID: <a1922ea9-4776-a450-7bea-5e141850f...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/15/18 12:31 PM, ABEL Stephane wrote:
> Hello,
>
> I have finally resolved my problem thank to Justin .

Would you be willing to share the exact sequence of events, commands,
etc. that worked? As I mentioned before, these threads often trail off
or end unresolved, so while it is nice that you solved your own problem,
it would be beneficial to the community to document how you did it so
that others might learn.

-Justin

> Bye
> --
>
> Message: 2
> Date: Sun, 14 Jan 2018 17:36:21 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide w

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

[ABEL Stephane]

Hello, 

I have finally resolved my problem thank to Justin . 

Bye 
--

Message: 2
Date: Sun, 14 Jan 2018 17:36:21 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <b7a10948-61d2-5b3f-b062-6630785c6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 12:04 PM, ABEL Stephane wrote:
> Thank you, Justin for your interest to my problem,
>
> But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
> ILE instead of a central a simple ILE :((

Ile should not be treated as a terminal residue, and it wasn't in the
screen output you provided before after adding your custom residues to
residuetypes.dat. That's a prerequisite if you want anything to work.
Getting the connectivity right after dealing with the custom residues is
the next problem after that.

-Justin

> *gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing
>
> I will try to search a workaround
>
> Best
>
> St?phane
>
> ____
> De : ABEL Stephane
> Envoy? : dimanche 14 janvier 2018 16:52
> ? : gromacs.org_gmx-users@maillist.sys.kth.se
> Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50
>
> Thanks Justin
>
> First I forgot to say that I am building a cyclic peptide (Atosiban, 
> https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
> (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since 
> the two residues are well constructed and linked together with pdb2gmx as it 
> is shown If I consider the ILE as NILE
>
> For linking the MER and CYX I define a bond with the specbond.dat (the 
> corresponding bond is shown in the  pdb2gmx output). The only problem I have 
> is that NILE residue is chosen instead of ILE
>
> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange 
> or I found a subtle error I cannot find.
>
> St?phane
>
>
>
>
> --
>
> Message: 3
> Date: Sun, 14 Jan 2018 10:34:08 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide with two
>  modified residues with amber ff
> Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:04 AM, ABEL Stephane wrote:
>> Hi Justin
>>
>> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
>> the the following output with pdb2gmx. I select 2 and 6
>>
>> ##
>> gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
>> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>>
>>
>> Select the Force Field:
>>   From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>>1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>>2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>>3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>>4: CHARMM36 all-atom force field (July 2017)
>>5: CHARMM36 all-atom force field, surfactants and pigments
>>6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. 
>> B 2011, 115, 487-499 )
>>7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
>> 3825?3850)
>>8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
>> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>>9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
>> 10.1002/jcc.21675)
>> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
>> 10.1007/s00249-011-0700-9)
>>   From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
>> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
>> 1999-2012, 2003)
>> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
>> 461-469, 1996)
>> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
>> 1049-1074, 2000)
>> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
>> 2006)
>> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., 
>> Proteins 78, 1950-58, 2010)
>> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for pro

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

[ABEL Stephane]

Thank you, Justin for your interest to my problem, 

But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
ILE instead of a central a simple ILE :((

*gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing

I will try to search a workaround 

Best 

Stéphane


De : ABEL Stephane
Envoy? : dimanche 14 janvier 2018 16:52
? : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

St?phane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> 

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

[ABEL Stephane]

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

De : ABEL Stephane
Envoyé : dimanche 14 janvier 2018 16:52
À : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

Stéphane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
> 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 50

[ABEL Stephane]

Thanks Justin 

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE 

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.  

Stéphane 


 

--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
> Reading Atosiban_box_ctr.pdb...
> Read 'GROningen MAchine for Chemical Simulation', 85 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 10 residues with 85 atoms
>
>chain  #res #atoms
>1 'A'10 85
>
&

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

[ABEL Stephane]

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
the the following output with pdb2gmx. I select 2 and 6

## 
  gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes


Select the Force Field:
From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
 1: Amber12sb ff99SB + new backbone and side chain torsion for protein
 2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
 3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969–1980)
 4: CHARMM36 all-atom force field (July 2017)
 5: CHARMM36 all-atom force field, surfactants and pigments
 6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
2011, 115, 487-499 )
 7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 3825−3850)
 8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. 
Chem. C, 2015, 119 (14), pp 7888–7899)
 9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2

Using the Amber14sb_parmbsc1 force field in directory 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat

Select the Water Model:
 1: TIP3P TIP 3-point, recommended
 2: TIP4P TIP 4-point
 3: TIP4P-Ew  TIP 4-point optimized with Ewald
 4: SPC   simple point charge
 5: SPC/E extended simple point charge
 6: None
6
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
Reading Atosiban_box_ctr.pdb...
Read 'GROningen MAchine for Chemical Simulation', 85 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 85 atoms

  chain  #res #atoms
  1 'A'10 85

All occupancies are one
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
Atomtype 89Reading residue database... (amber14sb_parmbsc1)

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
Residue 1
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
Residue 2
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
Residue 95
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
Residue 111
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
Residue 127
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb
Opening force field file 

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

[ABEL Stephane]

Dear all, 

I have a peptide with two modified residues at the Nter with the following 
sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified 
tyrosine  residue (side chain), respectively. the Mer, TYR and ILE are bonded 
together with a peptide bond. To build the corresponding force field compatible 
with Amber. I am using pdb2gmx  with the following command (gmx5.1.2): 

pdb2gmx -f mypeptide.pdb  -p topol.top -o  mypeptide.gro

the ILE residue are always recognized as the Nter residue of the peptide with 
NH3+ with the name NILE and thus I obtain the "dangling bond" error  Is it 
possible "to force" pdb2gmx to use a particular rtp entry (here the central ILE 
residue) and consequently build the correct peptide bond between the TYO and 
ILE residues?  Note that the name of the isoleucine residue in " mypeptide.pdb" 
is "ILE" and not NILE.

I have also use pdb2gmx -f mypeptide.pdb  -p  topol.top  -rtpres yes 

but it does not work either

Thank for your help

Stéphane
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[gmx-users] Problem with G_WHAM and -bsprof command (Justin Lemkul)

[ABEL Stephane]

Yeah you are right. It is working now

Thank you 


On 11/20/17 10:18 AM, ABEL Stephane wrote:
> hello everybody
>
> I am trying to obtain the average and SD of PMF profile with gmx wham (gmx 
> 5.1.2 and 2016.1) with the following command in a bash script
>
> mpirun -np 1 gmx_mpi wham -it Wham_TPR_step5.dat -if Wham_Pullf_step5.dat 
> -unit kCal -temp 298 -b $begin -e $end -hist "$NameFile"_"$Name"_hist.xvg -o 
> "$NameFile"_"$Name"_profile.xvg -bs-method hist -min 0.0 -max 5.6 -bsprof 
> "$NameFile"_"$Name"_profile_bsResult.xvg
>
> According to the manual, the -bsres  should ouput the "Average profile and 
> standard deviations". The calculations runs with no errors  but I do not 
> obtain "$NameFile"_"$Name"_profile_bsResult.xvg file. Am I missing something.

Probably the fact that -nBootstrap defaults to zero, so you need to
specify a real value if you want output from bootstrapping.

-Justin

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[gmx-users] Problem with G_WHAM and -bsprof command

[ABEL Stephane]

hello everybody

I am trying to obtain the average and SD of PMF profile with gmx wham (gmx 
5.1.2 and 2016.1) with the following command in a bash script

mpirun -np 1 gmx_mpi wham -it Wham_TPR_step5.dat -if Wham_Pullf_step5.dat -unit 
kCal -temp 298 -b $begin -e $end -hist "$NameFile"_"$Name"_hist.xvg -o 
"$NameFile"_"$Name"_profile.xvg -bs-method hist -min 0.0 -max 5.6 -bsprof 
"$NameFile"_"$Name"_profile_bsResult.xvg

According to the manual, the -bsres  should ouput the "Average profile and 
standard deviations". The calculations runs with no errors  but I do not obtain 
"$NameFile"_"$Name"_profile_bsResult.xvg file. Am I missing something.

Thank you 

Stéphane 
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[gmx-users] Conversion Amber to Gromacs

[ABEL Stephane]

Hello Elisa, 

"J'arrive après la bataille" To be sure that you have correct Amber parameters 
for GROMACS, you could also use the acpype suite*. This suite converts  Amber 
params in gromacs format. The program generates the (non)ffbonded.itp and top 
files in gromacs format from the Amber's LeaP tool. It also provides some 
gromacs and Amber files to perform and a single point energy to test if the 
conversion is correctly done. 

I used successfully this code  to convert the Amber lipid14 params for POPC 
lipid in the GROMACS format.

*http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder

HTH 

Stéphane  

--

Message: 3
Date: Tue, 24 Oct 2017 17:17:08 +0200
From: Elisa Pieri 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID:

[gmx-users] problems with difference in the COM distances in US sampling

[ABEL Stephane]

Hello 

I am trying to perform some US calculations to obtain the potential of mean 
force of the insertion of a molecule inside a lipid bilayer. For that I follow 
the tutorial of Dr Justin Lemkul with some modifications and start the 
simulations with the following mdp 

pull_group1_name= MEMB
pull_group2_name= FEI
pull_ngroups= 2
pull_ncoords= 1
pull-nstxout= 500
pull-nstfout= 500
pull_print_com1 = yes
pull_print_ref-value= yes
;pull_print_components   = yes
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple direction decrease
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_k = 1500
;pull_coord1_rate= -0.01
pull_coord1_start   = yes 

And indeed after 800 ps the molecule move to the bilayer center and  the 
distance between the COMs of the molecule and the bilayer reported in the pullx 
file is close 0 nm. 

However when I do the second step of the tutorial with the perl script provide 
in the  J. lemkul tutorial (perl_distance.pl) to select the US windows, the 
distance is greater than around 1 for the same config . see below

the pullx = 

800.0.00105624  -4.02734

the COM-distance computed with perl script  after the membrane was centered in 
the box with -pbc mol is 

800 1.264

Why  this difference, and to choose the good interval for the US sampling

I use the following command trough the perl script 

distance_PMF$ gmx_mpi distance -s 
./US_Files_step1/PHE_POPC_Memb_CHARMM_PMF_1500Kj_01rate_US_step1.tpr -f 
conf800.gro -n System.ndx -oall dist0.xvg -select 'com of group MEMB plus com 
of group FEI'



Thank you in advance

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[gmx-users] legend in the pulling file (gmx 5.1.4)

[ABEL Stephane]

Hi all, 

A quick question:

What are the meaniings of the s1 , s1 and s2 legends in the pullf.xvg? 

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (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 "1 c1Z"
@ s1 legend "1"
@ s2 legend "r1"

Thank you 

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[gmx-users] Topolgen and topolbuild

[ABEL Stephane]

Hi

if your molecule is a ligand, you could use ParamChem 
(https://cgenff.paramchem.org/) 

Stéphane

--

Message: 1
Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST)
From: Sergio Manzetti 
To: gmx-users 
Subject: [gmx-users] Topolgen and topolbuild
Message-ID:
<1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no>
Content-Type: text/plain; charset=utf-8

Hi, I found these tow programs on GMX site, however they don't work. How can I 
generate a CHARMM topology to be used in GMX for a charged molecule?

Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | 
Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | 
FAP ]
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 9

[ABEL Stephane]

Hi, 

In addition to my previous email

If you have all the parameters obtained from RESP and tleap program (mol2, 
frcmod and lib) you could use the ACPYPE program to obtain the itp file for 
GROMACS 

See  
http://www.shourjya.thinkbiosolution.com/assigning-point-charges-to-non-standard-molecules-for-md-simulation/

and http://webapps.ccpn.ac.uk/acpype/

Good luck


Stéphane Abel, Ph.D.

CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


--

Message: 3
Date: Tue, 3 Oct 2017 19:25:48 +0200 (CEST)
From: Sergio Manzetti 
To: gmx-users 
Subject: [gmx-users] Tutorial
Message-ID:
<1499903584.16707185.1507051548537.javamail.zim...@fjordforsk.no>
Content-Type: text/plain; charset=utf-8

Hi, is there a tutorial for importing fully charged non-peptid topologies for 
the AMBER FF ISBN type to GMX somewhere ?
Thanks

Sergio Manzetti

Fjordforsk AS
Midtun
6894 VangsnesNorge
Org.nr. 911 659 654
Tlf: +47 57695621?kolab  |  Nanofactory  |  AQ-Lab  |  FAP

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[gmx-users] Charges and Antechamber

[ABEL Stephane]

HI 

It is quite easy to derive RESP charges and use them with GROMACS. You could 
follow the steps

1) Build a pdb file of your molecule/modified residue 
2)  Use the web server pyRED 
(http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive the 
RESP charges. The webserver will also give you all the necessary parameters of 
the ff (mol2 file, atom types, (non)bonded parameters)
3) Use these parameters to construct a rtp file for GROMACS for a given force 
field
4) and finally use pdb2gmx with the pdb file to obtain the itp file.  

That's all 

Good luck 
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[gmx-users] Necessary files to restart/continue REMD

[ABEL Stephane]

Hello,

Two  quick questions about REMD 

1) What are the necessatry files to restart a REMD simulations with -append and 
-noappend arguments? I ask these question because if I do not provide a trr 
file, GROMACS crashs with a error related to the checksum of the trr

2) Can I use the argument -noappend with REMD simulations  ?

Thank you 

Stéphane


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Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved

[ABEL Stephane]

THank you Mark and Johannes, 

I finally resolved my problem by using your solutions and can launch my REMD 
simulations 

Best

Stéphane


--

Message: 1
Date: Wed, 02 Aug 2017 10:59:10 +
From: Mark Abraham <mark.j.abra...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)
Message-ID:
<camnumaqep0deuo08vqjyvtnpbbd3rjaawa2bd_czh377eea...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane <stephane.a...@cea.fr> wrote:

> Dear all,
>
> I would like to do a REMD of a system with 75 replicas (with 75
> directories named md_0,..., md_75) and I have two questions.
>
> 1) To launch the md calculation we should use the followng command :
>
> mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX
>
> My question is since I have 75 replicas (directories). How I should set
> the argument of -multidir ? Like this : -multidir md_[01234...75] or only
> "md_".
>

The -multidir option needs a list of all your directories. The best way to
do that is with shell (e.g. wildcard) expansion. Just using "md_" doesn't
get expanded by anything. I recently observed someone suggest that
"md_{0..75}" might do what you want, but I've never tried it. Anyway, md_*
will expand them all, and IIRC mdrun will sort out the ordering from the
values of the REMD control parameter.


> I have used the following command : mdrun_mpi -v -multidir
> ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the
> following error : Need at least two replicas for replica exchange (option
> -multi)
>

Since there's only one directory named, because the shell couldn't expand
anything for you, mdrun doesn't know how to proceed. Pro tip - get it
working for a small number of replicas (e.g. 2) before worrying about using
all 75.


> 2) Second question It is not clear to me how I should set the number of
> step in the mdp file of each replica use in the production runs.  For
> instance I want to do a simulation of 50 ns, should I set nsteps =
> 500/75
>

Each simulation is independent and every e.g. mdp parameter is particular
to it. So choose your number of steps in each mdp file to be the length of
a single replica. Obviously nsteps * dt = time in the usual way, but since
we don't know dt, you'll have to compute your nsteps ;-)

Mark

Could you help me ?
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[gmx-users] Error in the replica order in REMD (GMX v2016.1)

[ABEL Stephane]

Hello again

Thanks to J. Hermann  I can start my simulations, however few seconds after the 
beginning of the run I have the following error

"Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please order 
your replicas on increasing temperature"

I do not understand this error, since my replicas seem well ordered (i think) : 
ref_t in replicas 2 is 254.27 K  and ref_t in replicas 12 is 271.9) I check 
this with the ref_t in the mdp. For this calculation I used the cpt file to 
generate the tpr.

Could you help me again ?

Stéphane



   
Stéphane Abel, Ph.D.

CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C 
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
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[gmx-users] -multidir option in REMD (GROMACS v2016.1)

[ABEL Stephane]

Dear all, 

I would like to do a REMD of a system with 75 replicas (with 75 directories 
named md_0,..., md_75) and I have two questions. 

1) To launch the md calculation we should use the followng command : 

mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX

My question is since I have 75 replicas (directories). How I should set the 
argument of -multidir ? Like this : -multidir md_[01234...75] or only "md_". 

I have used the following command : mdrun_mpi -v -multidir 
./"$Stage1_FileName"/md_ -replex 500, but the program stops with the following 
error : Need at least two replicas for replica exchange (option -multi)

2) Second question It is not clear to me how I should set the number of step in 
the mdp file of each replica use in the production runs.  For instance I want 
to do a simulation of 50 ns, should I set nsteps = 500/75

Could you help me ? 

Thanks for your help

Stéphane
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[gmx-users] topology servers versus ff

[ABEL Stephane]

Hello,

If you want to use CHARMM for your simulations, do not use PRODRUG to construct 
your parameters but use ParamChem, instead. 

https://www.paramchem.org/

Stéphane

--

Message: 2
Date: Wed, 12 Jul 2017 14:36:27 +0500
From: maria khan 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] topology servers versus ff.
Message-ID:

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

Dear gromacs users..

while using charmm27 can i use PRODRUG for topology building.??

when im using prodrug pdb2gmx gives me error of missing atoms but when i
use charmm ff,it doesnt give me that error,so proceeding with charmm27 i
made ligand topology by prodrug and used it for further simulation,when
comes to adding ions step it gives me error of ""atomtypes CH3 not found"".

thanks.


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End of gromacs.org_gmx-users Digest, Vol 159, Issue 58
**
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[gmx-users] topology file with virtual site for an asymetric linear molecule

[ABEL Stephane]

Dear all,

I would like to use the virtual site capability of GROMACS to construct the 
topology of an asymmetric linear molecule (say SeCN). Does somebody have an 
example of topology file for a similar molecule to share with me? 

Thank you 

Stéphane
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[gmx-users] an error related to Gromacs version

[ABEL Stephane]

Hello, 

Probably you used a tpr file does not compatible with an older version of 
GROMACS. To resolve this problem, you could generate a new tpr with  Gromacs 
5.0.7 and use it for your free energy calculations 

HTH

--

Message: 4
Date: Sun, 25 Jun 2017 05:05:53 + (UTC)
From: Mahboobeh Eslami 
To: Discussion List for GROMACS Users 
Subject: [gmx-users] an error related to Gromacs version
Message-ID: <162816243.1216852.1498367153...@mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hi all GMX usersI did MD simulation by Gromacs 5.1.2 and I want to calculate 
free energy by GMXPBSA script. This script don't work correctly with Gromacs 
5.1.2 so I have to done free energy calculation by Gromacs 5.0.7. If I do this 
calculation I will get an error related to Gromacs version. Is there any way to 
solve this problem?Please help me
thanks


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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 49

[ABEL Stephane]

Hello Xujun

>>Could someone give me some suggestion on choosing one typical type of bile 
>>salts for the study? Which force field is better?
You will to read first some biological/physiological textbooks. Moreover, bile 
salts are complex molecules and probably difficult to model. so I would suggest 
to read also literature and see what types of bile salt were already 
simulated/studied and thus choose the the force field accordingly. 

HTH

Stéphane from Paris ;)

--

Message: 1
Date: Thu, 8 Jun 2017 14:26:26 +0800
From: "=?ISO-8859-1?B?bHhqMjU4Ng==?=" 
To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="

Subject: [gmx-users] Enquiry about simulating the aggregation behavior
of  bile salts in GROMACS
Message-ID: 
Content-Type: text/plain;   charset="ISO-8859-1"

Dear users,


I am planing to simulate how small organic molecules (i.e. pyrene and 
phenanthrene) bind to bile salts in the gut using GROMACS. However, there are 
diverse groups of bile salts in the intestinal systems. Could someone give me 
some suggestion on choosing one typical type of bile salts for the study? Which 
force field is better?


Many thanks for your time and help!


Sincerely yours,


Xujun Liang


--
Xujun LIANG, PhD
 School of Environment and Energy
South China University of Technology
Guangzhou, 510006
Guangdong Province
China


 Best wishes to you!!
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[gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

[ABEL Stephane]

Hello, 

You could write a proposal to have access to the supercomputers of the PRACE 
consortium |1]. The access to the machines is free,

[1] http://www.prace-ri.eu/

Stéphane


--

Message: 3
Date: Mon, 15 May 2017 14:45:00 +0200
From: Jo?o Henriques 
To: gmx-us...@gromacs.org
Subject: [gmx-users] HPC resources in Europe (preferably
Northern/CentralEurope)
Message-ID:

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

Dear users and developers,

Our research group is having trouble finding enough computational resources
to run our GROMACS simulations and it was decided that I would be in charge
of finding new alternatives. I know this topic is not 100% GROMACS related
in a strict sense, but I've seen threads about similar topics in the past
and thought it would be a good idea to give it a shot, since there are
many, many researchers and PIs who read/participate in this list.

We have access to a couple of "supercomputers" in our area, but due to
heavy booking and some other technical issues, several postdocs and
students are struggling to get their simulations performed within in a
reasonable amount of time. Does anyone know of any HPC clusters within the
aforementioned geographic region which we could apply for/rent/buy computer
time?

Any input would be greatly appreciated.

Thank you,
Best regards,
Jo?o
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[gmx-users] Save the velocities a subset of atoms in a trr file during a simulation

[ABEL Stephane 175950]

ello, 

A quick question : 

It is possible to save the velocities (in a trr file) for only selected atoms 
"during" a simulation as we can do in case of  the xtc files by using a the mdp 
option compressed-x-grps?   

Thanks

S
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[gmx-users] PBC issues with membrane-peptide simulation

[ABEL Stephane 175950]

Hi, 

it is not an issue !! To resolve your problem you could simulate two bilayer in 
box and  insert the peptides between them. 

HTH

--

Message: 6
Date: Wed, 9 Nov 2016 16:07:26 +0530
From: Abhi Acharya 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
Message-ID:

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

Dear Gromacs users,

I am trying to simulate a system consisting of a lipid bilayer and few
peptides. The peptides have been added randomly to the simulation box only
on one side of the membrane. I ran a 100 ns simulation of the system using
CHARMM36 forcefeild. However, I find that within the first few ns, some of
the peptides appear on the other side of the membrane. I think that this is
because of the diffusion of the peptides though the periodic boundary.
Kindly suggest  how to tackle this problem. I have used COM motion removal
on the whole system for the said simulation.

Regards,
Abhishek Acharya


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[gmx-users] problem with backward to construct a CHARMM36 model

[ABEL Stephane 175950]

Dear all, 

Sorry in advance if the following message does not follow the netetiquette (my 
message was already post in the Martini forum) but since more gromacs users 
read this mailling list than the Martini one, I think that probably some users 
may help me to resolve my problem.  

I am interested to transform a CG surfactant system that contains AOT* into 
atomistic (with the charmm27/36 rules). For that I have built my own map file 
and used it with the python scripts backward.py with the following command line

./initram.sh -f 1_AOT_CG.gro -kick 0.5 -o 1.5us_AOT_RM_CG_AA.gro -p 
System_AA.top -from martini -to charmm36 -nopr -nb 1000 -em 1000 -keep

The 1_AOT_CG.gro file contains 1 AOT CG molecule. The  script  works well at 
the beginning without any errors  but no  0-backward.gro file with the 
projected coordinates is generated and consequently the script stops durin the 
minimization steps

I have a probably an error in my *.map file  but I do not know where

Could you help me? You could download the necessary files to have an idea by 
clicking on the following link:

https://drive.google.com/file/d/0B3sW6cS-tVa2TXZWa2hpVFpEdG8/view

* pubs.rsc.org/en/content/articlehtml/2014/sm/c4sm01763c

Thanks in advance and sorry again for the double post

Stéphane




   
Stéphane Abel, Ph.D.

CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C 
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
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[gmx-users] Reaction Field approach with GROMACS

[ABEL Stephane 175950]

Hi All, 

I have a question about the reaction field approach used by GROMACS. I have 
seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the 
Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is 
corrected in the GROMACS version than 5.0 or in lastest version one (e.g. 
2016)? Can I use safely this approach to compare my results with those obtained 
with the GROMOS program?

Thanks

Stéphane
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[gmx-users] grompp not enough parameters

[ABEL Stephane 175950]

Hi Marlon, 

If you change the comma into a point in the force constant values it should 
work  

Good luck



Hello,

I'm trying to use the amber03 ff to simulate a protein with iron clusters.
I got the right parameters from a paper but then grompp tells me:
"ERROR 1 [file clusters_ffbonded.itp, line 53]:
  Not enough parameters


ERROR 2 [file clusters_ffbonded.itp, line 54]:
  Not enough parameters


ERROR 3 [file clusters_ffbonded.itp, line 55]:
  Not enough parameters


ERROR 4 [file clusters_ffbonded.itp, line 56]:
  Not enough parameters


ERROR 5 [file clusters_ffbonded.itp, line 57]:
  Not enough parameters"

The thing is, line 53 to 57 from this file is the dihedrals for one of the
clusters:
"SEHSFEHSSH  CT   9   0.0 8,5772  3
FEHSSEHSFEHSSH   9   180.0   16,150245
SEHSFEHSNA  CR   9   180.0   5,69024 3
SEHSFEHSNA  CC   9   0.0 5,69024 3
FEHSSEHSFEHSNA   9   180.0   4,26768 5"

I don't understand where there are missing parameters. Indeed, a classical
line from the dihedrals of ffbonded.itp has the same number of parameters,
for example:
" C   N   CT  C 9 180.0  1.44390 2  ; Amber03"

Did any of you run into this before ?

Best regards,

Marlon Sidore


PhD Student
Laboratoire d'Ing?nierie des Syst?mes Macromol?culaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France

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Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

[ABEL Stephane 175950]

Hi,  

Before to compute the partial charges , you have to optimize the molecule. It 
may be very difficult if you have a large molecule (> 100 atoms). So for 
polymers with reapeated units, it is always advisable to separate the molecule 
into similar molecular blocks. It is straighforward for pluronic f127.  To 
derive charges for AMBER simulations, you can use the RED server* and checkout 
the detailed tutorials. It is an advanced topic  

http://upjv.q4md-forcefieldtools.org/REDServer-Development/ 

Good luck, 



Stéphane Abel, Ph.D.

CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


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Today's Topics:

   1. Re: top parameters for pluronic f127 (Andrian Saputra)
   2. Re: top parameters for pluronic f127 (Andrian Saputra)


--

Message: 1
Date: Sun, 5 Jun 2016 10:52:52 +0700
From: Andrian Saputra 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] top parameters for pluronic f127
Message-ID:

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

I have the same problem.. but gasteiger is less accurate... anyone can
suggest software quickly generating am1bcc, resp, esp charges for big
molecules ?
Pada tanggal 4 Jun 2016 00.51, "Alan"  menulis:

> It's too big! It will never work.
>
> Try the following alternatives:
> - to use gasteiger charge (and then you get only the topology);
> - as you said it's a polymer, take the smallest common unit, join 3 pieces
> of it and get the topology/charges for it, use the middle unit to extend
> the charge for all internal units of your polymer and the extreme to model
> your terminals.
>
> Good luck,
>
> Alan
>
> On 3 June 2016 at 18:37, SAKO MIRZAIE  wrote:
>
> > Dear All,
> >
> > I am trying to convert my mol2 file to amber99sb itp to do MD by
> > gromacs. but, when I use ACPYPE software, it run and never finished.
> > my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> > is a polymer and huge in size. how can I get an itp file for my
> > polymer? How can I simulate it in MD by gromacs? do polymers have some
> > tricks?
> >
> > the molecular structure of f127 is: A99B67A99
> >
> > where
> >
> > A: ethylene oxide
> > B: propylene oxide
> >
> > best regards,
> >
> > --
> > ***
> > sako mirzaie
> > PhD in biochemistry
> > --
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> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
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>


--

Message: 2
Date: Sun, 5 Jun 2016 11:30:32 +0700
From: Andrian Saputra 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] top parameters for pluronic f127
Message-ID:

[gmx-users] Angle between a vector and the normal to a sphere

[ABEL Stephane 175950]

OK  thanks Yu,  

I have another question how to select the  water sphere  center dynamically  
With g_select?  

S

- 

Hi St?phane,
gmx gangle may be what you need.
http://manual.gromacs.org/programs/gmx-gangle.html
-Yu

2016-05-31 13:22 GMT+02:00 ABEL Stephane 175950 <stephane.a...@cea.fr>:

> Hi all,
>
> Is there a command/tool in a gromacs to compute the angle between a vector
> defined defined two atoms molecule and the normal to a sphere defined by a
> set of atoms for instance water ? if yes, how
>
> I use a version of gromacs > 5.0
>
> Thanks
>
> St?phane
>
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[gmx-users] Angle between a vector and the normal to a sphere

[ABEL Stephane 175950]

Hi all, 

Is there a command/tool in a gromacs to compute the angle between a vector 
defined defined two atoms molecule and the normal to a sphere defined by a set 
of atoms for instance water ? if yes, how 

I use a version of gromacs > 5.0 

Thanks

Stéphane

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Re: [gmx-users] update .hdb file

[ABEL Stephane 175950]

Hello Shahla, 

We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table 
file for you with any rtp file. Please contact me contact me off list if you 
are interested

Best  

--

Message: 5
Date: Sat, 9 Apr 2016 08:49:05 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org, Shahla Omidi 
Subject: Re: [gmx-users] update .hdb file
Message-ID: <5708fa41.2060...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 4/9/16 1:55 AM, Shahla Omidi wrote:
> ?Hi
> I want to simulate a glycoprotein, I have defined a new residue with charmm36
> inorder to update the .hdb file, I need to define the order of atoms that are 
> conecting to atoms that is conecting to H atoms in my new residue
> but I dont exactly know about the standard format of showing atoms connection 
> to   atoms.
> Is the order of them relate to their distance from the n terminal or is 
> another standard to show which connected should come first?
> for example:
> HB  CB  CG  CA
> and
> HB  CB  CA   CG
> which one is true?
>

Read the manual, section 5.7.4.

-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] pdb2gmx error

[ABEL Stephane 175950]

Indeed Justin I have tried to add  the entries for the capped groups in the 
Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present 
in  aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken 
something 

Stéphane


On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote:
> Hello,
>
> When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN 
> force field, I have the error :
> Fatal error:
> tpA = 53191, i= 0 in print_atoms
>
> I have no idea what does this message mean. Could you help me?
>

This shouldn't happen.  Have you or anyone else modified the code or force field
files?  That's the only instance in which this would be triggered.

-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] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

[ABEL Stephane 175950]

Hello again

I have noticed that in case of the amber* forcefields (in gromacs v504) the 
aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to 
construct easily a capped AA with the pdb2gmx -ter command without using a rtp 
file (and it is very painful). So does anyone have the modified (uptated) 
aminoacids.n.tdb and aminoacids.n.tdb files that contains the capped entries 
that in charmm distribution  

*This limitation was also discussed in the following thread 

http://comments.gmane.org/gmane.science.biology.gromacs.user/69523

Thanks

Stephane
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[gmx-users] pdb2gmx error

[ABEL Stephane 175950]

Hello, 

When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force 
field, I have the error : 
Fatal error:
tpA = 53191, i= 0 in print_atoms

I have no idea what does this message mean. Could you help me? 

Thanks 
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[gmx-users] infinite force at the membrane lipid

[ABEL Stephane 175950]

Hello,

How did you construct your membrane, with CHARMM-GUI? What is the lipid? From 
my experience, I have found that sometimes CHARMM-GUI does not provide a good 
starting point for MD. So I would suggest you to : 

- center the lipids inside the box to have no lipids that cross the box limit 
and/or increase a little bit the box size (x-y) and minimize  your system 
again. 

Moreover to insert you protein inside the membrane, did you try the inflate_gro 
or g_membed tools ?

Good luck

HTH

--

Message: 1
Date: Sun, 16 Aug 2015 10:51:42 +0900
From: Vy Phan phanvy120...@gmail.com
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] infinite force at the membrane lipid
Message-ID:
CAC+3Te00hidSrXE49g5mfqvCsBSaE5wTJ-NtFubaXvvz=u6...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

Dear Dr Justin and Gromacs User,

This is my commands for running energy minimization.

define  = -DPOSRES
integrator  = cg

nstcgsteep  = 1000
emtol   = 100.0
emstep  = 0.01
dt  = 0.002
; Output control
nstxout = 50
nstenergy   = 50
nstlog  = 50


nstlist = 1
cutoff-scheme   = Verlet
ns_type = grid
coulombtype = PME
rcoulomb= 1.2
vdw-modifier= Potential-shift
rvdw= 1.2
rvdw-switch = 1.0
pbc = xyz


I hope you can give more recommendations. Removing lipids actually is not
an appropriate solution.

Thank  you so much

Tuong Vy

2015-08-16 1:47 GMT+09:00 Justin Lemkul jalem...@vt.edu:



 On 8/15/15 12:41 PM, Vy Phan wrote:

 Dear All gromacs Users,

 I want to run the membrane protein simulation. I run the energy
 minimization for membrane and protein separately.
 After that I combine protein  and lipid together and remove the
 overlapping
 molecules.
 when I run energy minimization I got the error inf at atom on lipid. I
 remove the lipid which includes this atom.  I got the error several time
 and I repeat remove lipid. I see the inf at atom on lipid always happens
 on lipids which locate at the wall (at the boundary of unit cell).

 I successfully run one time when I remove  lipids have error, another was
 failed.

 I wonder why the error inf at atom on lipid always happens on lipids
 which locate at the wall. Maybe I did something wrong about periodic
 boundary condition.

 Thank you for any thoughts.


 Without a list of your exact commands and what you've done to this point,
 it's impossible to diagnose.  There's something fundamentally wrong with
 the coordinates, topology, or both.  If the infinite force is just moving
 around, what you're observing is a symptom, not a cause, and removing
 lipids to try to make it go away is not an appropriate solution.

 -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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End of gromacs.org_gmx-users Digest, Vol 136, Issue 75
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[gmx-users] Reverse micelle clustering issue

[ABEL Stephane 175950]

Hello

To center your RM inside teh box you could use to successive trjconv commands 
with pbc cluster and mol

in index.ndx

0 : all  
1 AOT 
2 water
3 AOT_Water
4 ISO

1 -- select  1 1 0 (or 2 2 0) 

echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur compact 
-center -o my_clustered,xtc 

2 - 2 0 (or 1 0) 

echo 1 0  | trjconv -f my_clustered,xtc -s my_tpr.tpr -pbc mol  -ur compact 
-center -o my_all_centered,xtc 

With these commands, the RM should be inside  the box 

BTW; 

Your box is a bit too small for me, What is the isooctane mass fraction ?

HTH

Stephane

--

Message: 3
Date: Tue, 21 Jul 2015 17:38:30 -0300
From: V.V.Chaban vvcha...@gmail.com
To: gmx-users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Reverse micelle clustering issue
Message-ID:
capxdd+avsj3pks0+csycatgp1tsod9b-rqjxbetk+aytsjj...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

The general advice to use trjconv  with every keyword independently.

In certain cases, its behavior is fairly bizarre if one uses all
keywords at the same time. Probably, order of called procedures in the
code matters...


Professor Vitaly V. Chaban




On Tue, Jul 21, 2015 at 3:08 PM, Tyler Cropley tyler.crop...@wagner.edu wrote:
 Dear Gromacs users,


  We ran a simulation of an AOT reverse micelle in isooctane solvent. We
 followed instructions
 http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering . For
 clustering we selected the group that contains AOT and for output we
 selected the entire system. The reverse micelle appears outside of the
 solvent box in vmd. This is the picture
 http://s24.photobucket.com/user/tycropley/media/RM-issue_zpsbngarszw.png.html
 . We used -center and -boxcenter for trjconv but it did not work.


  Is there a way to ensure that the corrected trajectory displays the
 reverse micelle inside the solvent box? Or is there something more
 seriously wrong?


  Thank you,

 Tyler
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--

Message: 4
Date: Tue, 21 Jul 2015 17:16:41 -0500
From: Krzysztof Kuczera kkucz...@ku.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS 5.0.5 GPU version on K620
Message-ID: 55aec4c9.5070...@ku.edu
Content-Type: text/plain; charset=utf-8; format=flowed

Hi Szil?rd ,

The test case worked after I added the flags you recommended, though the
speed was not as high as I had hoped - equivalent to about 6 CPU cores -
I guess my GPU is not so hot.

Below is the output from mdrun -version.  Please let me know if you
see things that might be optimized there.

Thanks for your excellent help!

Krzysztof
---
Gromacs version:VERSION 5.0.5
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled GPU support:enabled invsqrt
routine:gmx_software_invsqrt(x)
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.4-fma-sse2-avx RDTSCP usage: enabled C++11
compilation:  disabled TNG support:enabled
Tracing support:disabled
Built on:   Tue Jul 21 16:25:29 CDT 2015
Built by:   kuczera@lolipop-chem-ku-edu [CMAKE]Build
OS/arch:  Linux 3.10.0-229.4.2.el7.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W v3 @ 3.10GHzBuild CPU
family:   6   Model: 63   Stepping: 2Build CPU features: aes apic avx
avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm m
mx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apicC compiler: /usr/bin/cc GNU
4.8.3C compiler flags:-march=core-avx2 -Wno-maybe-uninitialized
-Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3
-DNDEBUG -fomit-frame-pointer -funroll-all-
loops -fexcess-precision=fast  -Wno-array-bounds
C++ compiler:   /usr/bin/c++ GNU 4.8.3
C++ compiler flags:  -march=core-avx2-Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function  -O3 -DNDEBUG -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
Boost version:  1.53.0 (external)
CUDA compiler:  /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
CUDA compiler

[gmx-users] command line with gangle

[ABEL Stephane 175950]

Hello all, 

I have a stupid question :

I would like to use gangle (v5.0.4) with the following command line 

gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n 
paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav test_angle.xvg 
-b 39000 -e 4  test_angle.txt

Without the test_angle.txt file I need to press the following buttons for 
selecting the group 0 and 3 

0 Enter Ctrl-D 3 Enter Ctrl D. 

How to include these commands in a text file (e.g.  test_angle.txt)  for that 
the calculation starts automatically (i.e. for instance with a bash script)

Thanks in advance for your help

Stéphane
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[gmx-users] command line with gangle

[ABEL Stephane 175950]

Many thanks, Teemu

it works 

Stephane
--

Message: 3
Date: Fri, 20 Mar 2015 18:05:49 +0200
From: Teemu Murtola teemu.murt...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] command line with gangle
Message-ID:
CAB5URpZEXrvBNBC0YqPuHXJmuhFs0THX+e=0thyrosu8aqf...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

By far the simplest method is to just pass your selections as command line
arguments, without any files:

  gmx gangle ... -group1 0 -group2 3

One goal for the selection implementation was that it's not necessary to
play around with complicated redirections to automate things.

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[gmx-users] how to remove water molecule inside micelle

[ABEL Stephane 175950]

Hello, 

It is not a really problem, since the water will move during the simulation 
(due to the hydrophobic effect), but It may take for that all the water left 
the micelle center. So I suggest you to use genbox with the following arguments 
 -shell or -vdwd (see the genbox manual). 

An other approach if you use Packmol to construct your micelle is to reduce the 
space between the SDS alkyl chains during the construction process by palying 
with the value in the inside command in your packmol script  

#  atoms 39 is the last Carbon of the C12 alkyl chain for  CHARMM
   atoms 39
   inside sphere 0. 0. 0. 3.0  --- 3  is the distance (in A) between the 
micelle center and the 12th carbon of the SDS alkyl chain.  [1]
  end atoms

[1] -  2-3 is a good value if you want to construct a SDS micelle with 60 
monomers
- You will need the minimize carrefully the micelle to remove steric clashes 
between SDS chains  

HTH

--

Message: 3
Date: Mon, 29 Dec 2014 11:09:18 +0330
From: Mina Hashemi hashemi.mi...@gmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] how to remove water molecule inside micelle?
Message-ID:
CAFYjG+ad2XDVy3PEO9Xnd6E9=n6qsv9srgtkk8sjr0honoh...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Dear gromacs users

I prepared my simulation system containing SDS.

Then I added water molecules using genbox. Some water molecules
entered in to the micelle.

How to remove water molecules inside the micelle?

Any help will highly appreciated.

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[gmx-users] Naughty Vacuum Bubble in our Vesicle

[ABEL Stephane 175950]

Hello Bjorn

I don't know if it related to your problem, but I see a typo in our mdp file 
for the pressure coupling: 

Pcoupltype   = isotropic ;semiisotropic   
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 4.0  4.0  
compressibility  = 3e-5 3e-5
ref_p= 1.0  1.0

You should have only one value for tau_p, compressibility and ref_p if you want 
to use an isotropic pressure coupling scheme in simulation (and two in case of 
semiisotropic). Strange that grompp did not mention this error.

HTH

Stephane
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[gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

[ABEL Stephane 175950]

Hello all, 

I am trying to convert some GLYCAM parameters to do simulations with the 
GROMACS code. In the glycam force field, several dihedral terms have negative 
barrier height values, for instance, -20 in the following parameter:  

 Os-Cj-Cj-Ha   1  -20.00  0.0 2  SCEE=1.0 SCNB=1.0 
copy of Os-Ck-Ck-Ha

So I wonder if  It is safe to use a negative value in case of GROMACS  for the 
amplitude 

;i   j   k   l   func  phi0cp  mult
 Os-Cj-Cj-Ha   9 0.0 -83.6802

Sorry if it is a stupid question and thanks in advance for your response

Stephane
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[gmx-users] Use trjconv in parallel,

[ABEL Stephane 175950]

Hello, 

in short : it is possible ? I use the gromacs v4.6.5. 

Thanks 

Stéphane
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Re: [gmx-users] Use trjconv in parallel

[ABEL Stephane 175950]

Thanks for your quick and also fast (;)) reply, Carsten. 

Stéphane


--

Message: 4
Date: Wed, 2 Jul 2014 10:55:45 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
To: gromacs.org_gmx-users@maillist.sys.kth.se
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Use trjconv in parallel,
Message-ID:
3e39b768bb199548ab18f7289e7534af1b24f...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=iso-8859-1

Hello,

in short : it is possible ? I use the gromacs v4.6.5.

Thanks

St?phane

--

Message: 5
Date: Wed, 2 Jul 2014 13:44:08 +0200
From: Carsten Kutzner ckut...@gwdg.de
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Use trjconv in parallel,
Message-ID: 39b862ce-6e52-4590-9c57-ba34864b2...@gwdg.de
Content-Type: text/plain; charset=iso-8859-1


On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello,

 in short : it is possible ? I use the gromacs v4.6.5.
No.

Carsten

 Thanks

 St?phane
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 mail to gmx-users-requ...@gromacs.org.



--

Message: 6
Date: Wed, 02 Jul 2014 07:50:34 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] grompp does not find atomtype
Message-ID: 53b3f20a.7060...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 7/2/14, 4:40 AM, Dawid das wrote:
 I have managed to deal with this problem in following way:

 In topology file some bonding parameters were actually missing but some
 bonding parameters were not needed, e.g. U-B or dihedral parameters for
 atoms which are not connected, that is they belong to different parts of my
 new residue.
 I found parameters for the missing ones and hashed (;) them out. Is it what
 I can do? Like I say, theses bonding parameters that I hashed out were for
 atom types which are not connected directly.

 Then I performed minimization with steepest descent and in output file I
 got:

   4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep=  426, Dmax= 2.5e-06 nm,
 Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep=  427, Dmax= 1.2e-06
 nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M
 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  1000

 Double precision normally gives you higher accuracy.
 You might need to increase your constraint accuracy, or turn
 off constraints alltogether (set constraints = none in mdp file)

 writing lowest energy coordinates.

 Steepest Descents converged to machine precision in 428 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  = -4.5465475e+05
 Maximum force =  1.7057922e+04 on atom 1003
 Norm of force =  1.1677969e+02

 But I continued with NVT MD simulation. This is my nvt-md.mdp file:

 title   = NVT MD
 integrator  = md
 constraints = all-bonds
 dt  = 0.001
 nsteps  = 2
 nstenergy   = 100
 nstlist = 10
 nstxout = 1000
 nstvout = 1000
 nstfout = 0
 nstlog  = 100
 nstxtcout   = 1000
 xtcprecision= 500
 ns_type = grid
 coulombtype = PME
 rlist   = 1.0
 rcoulomb= 1.0
 rvdw= 1.0

These cutoffs are incorrect for using CHARMM force fields.  See previous posts
on proper settings.

 tcoupl  = nose-hoover
 tc-grps = Protein SOL NA
 tau_t   = 0.1 0.1 0.1 ;(3 numbers - because 3 tc-grps)
 ref_t   = 100 100 100 ;(3 numbers - because 3 tc-grps)

Coupling water and ions separately is not sensible.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

 Pcoupl  = No
 gen_vel = yes
 gen_temp= 100
 gen_seed= 173529
 energygrps  = Protein  SOL NA
 constraint_algorithm = LINCS
 pbc = xyz

 And in my NVT output I got error for LINCS:

 relative constraint deviation after LINCS:
 rms 0.036755, max 1.509884 (between atoms 998 and 1000)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
 1001   1003   62.10.1410   0.2032  0.1410
 1001   1002   68.10.1240   0.1962  0.1240
 1000   1001   88.10.1460   0.3276  0.1460
  998   1000   90.00.1390   0.3489  0.1390
  986   1000   90.70.1400   0.2237  0.1400
  985986   30.70.1300   0.1499  0.1300
 Wrote pdb files with previous and current coordinates


 These atoms are those for my new residue. For next step

Re: [gmx-users] Simulations in NVE ensemble with CHARMM36 - update

[ABEL Stephane 175950]

Hello Justin

Thanks for your reply. I have finally found why I obtained a large drift and 
decrease of the temp of my system during the NVE : I stupidly mixed different 
cpt and tpr files. If I use the right files and the following parameters below 
suggested by M. Shirts in  [1] for my tests:

rlist   = 1.3
;vdW
vdwtype = Switch
rvdw= 1.1
rvdw_switch = 1.0

; Electrostatics
coulombtype = PME
rcoulomb= 1.3

The energy and the temp of my system remain stable during the 100 ps of my 
simulation after  initial small decrease of the energy and the temp to 295.5 K 
(initial temp was 297.904 K)

[1] http://comments.gmane.org/gmane.science.biology.gromacs.user/42686

Please also note that with the parameters for Verlet options you gave I obtain 
the following error with 4.6.5 for simulations with NVE, 

 Temperature coupling is required for calculating rlist using the energy
  drift with verlet-buffer-drift  0. Either use temperature coupling or
  set rlist yourself together with verlet-buffer-drift = -1

If I add the verlet-buffer-drift = -1 option in my mdp (not sure it is 
correct), grompp gives only two notes 

NOTE 1 [file run_CH_1_NVE_pot_mod.mdp]:
  With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.


NOTE 2 [file run_CH_1_NVE_pot_mod.mdp]:
  rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
  buffer. The cluster pair list does have a buffering effect, but choosing
  a larger rlist might be necessary for good energy conservation.


Stéphane


On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:
 Dear GMX-users

 I have done a 90 ns long simulation of a heterogeneous  system (SPCE water, 
 phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) 
 with GROMACS4.6.5. to compute related dynamical properties, I would like to 
 continue this simulation in NVE. But I am puzzled to choose the mdp 
 parameters to have a good energy conservation. Indeed, I have checked the 
 gromacs 2004 JCTC or the following and follow the advices given in the 
 following threads

 http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
 https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html

 But I always obtain for my system a large drift and the temp decreases 
 significantly (20 K) after few dozens of ps (the initial temp was around 
 297.3 K). For this simulation I used the double precision of gromacs with a 
 timestep of 1 fs.


Can you provide a full .mdp file so we can look at all your settings?  Are these
drifts during NPT or NVE?

 More, since I have never used the potential-modifier features, so I not sure 
 how to setup  the correct parameters in the context of CHARMM simulations.


With the caveat that I have NOT thoroughly tested the following, my
understanding of the new Verlet options indicates that these settings should
perform pretty well using CHARMM36:

cutoff-scheme = Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2

Again, barely tested on my part, and never tested for NVE.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Simulations in NVE ensemble with CHARMM36

[ABEL Stephane 175950]

Dear GMX-users

I have done a 90 ns long simulation of a heterogeneous  system (SPCE water, 
phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with 
GROMACS4.6.5. to compute related dynamical properties, I would like to continue 
this simulation in NVE. But I am puzzled to choose the mdp parameters to have a 
good energy conservation. Indeed, I have checked the gromacs 2004 JCTC or the 
following and follow the advices given in the following threads

http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html

But I always obtain for my system a large drift and the temp decreases 
significantly (20 K) after few dozens of ps (the initial temp was around 297.3 
K). For this simulation I used the double precision of gromacs with a timestep 
of 1 fs. 

More, since I have never used the potential-modifier features, so I not sure 
how to setup  the correct parameters in the context of CHARMM simulations. 

Could you help and provides some advices

Thanks

Stephane
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[gmx-users] conversion xtc to xyz format with openbabel

[ABEL Stephane 175950]

Hello all,

My apologies for these  out topic questions 

 Does anybody have already try to convert xtc trajectory into xyz with 
openbabel? 

Btw, it seems that pdb file generated with editconf can not be read by 
openbabel. I obtain the following error : 

 WARNING: Problems reading a PDB file
  Problems reading a HETATM or ATOM record.
  According to the PDB specification,
  columns 77-78 should contain the element symbol of an atom.
  but OpenBabel found '  ' (atom 1)


Does anybody have a workaround?

Thanks in advance



Stéphane Abel, PhD
CEA Saclay DSV/IbItec-S/SB2SM  CNRS UMR 8221
Bat 528 Door 138C  
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
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