[gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. To achieve the same, I used the following command: $g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral I got the desired output. However, the output shows angles ra

Re: [gmx-users] Does .xtc enough for all kind of analysis?

Daily reminder that *Google is your friend*! See ---> http://manual.gromacs.org/online/files.html Honestly, I can't think of a single analysis that requires the .xtc only, or even the .trr for that matter. Most analysis tools need to know about the system topology among other things. Still, if di

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Hi, I'm assuming you are measuring more than one dihedral (since you are using the -all option). So assuming columns 2 to 5 correspond to the measured dihedrals: awk '{print $1,($2+180),($3+180),($4+180),($5+180)}' angaver.xvg > new_ angaver.xvg This should do the trick. Regards, On 10 Septe

Re: [gmx-users] Multiple membrane proteins in complex bilayer (martini)

Hi Kathrin, if I remember correctly I once did something similar with g_membed -pieces ! Cheers, Dr. Jan-Philipp Machtens Institute of Complex Systems - Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich, Germany Telefon: 02461 616467 ===

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

I do not think gmx angle supports this, but it very easy to just add 180 to xvg files. 1) One approach is to edit the data file prior to plotting. Issue this command: awk "{if (/@|#/){print}else{print $1+180,$2}" angdist.xvg > angdist360.xvg 2) With gnuplot you can use this command to plot and

[gmx-users] naming of CH2 groups in pdb file

Dear Gromacs users, I have built a pdb file format for a polymer, and I want to use GROMOS FF. Therefore, I included polar Hydrogens in the pdb file, but I do not know how to name CH2 groups in NAME and SEGNAME columns. When executing the pdbtogmx command I receive the following error: Residue 2 n

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Thank you very much. That was helpful. Regards, Gayathri S. > Hi, > > I'm assuming you are measuring more than one dihedral (since you are using > the -all option). So assuming columns 2 to 5 correspond to the measured > dihedrals: > > awk '{print $1,($2+180),($3+180),($4+180),($5+180)}' angav

Re: [gmx-users] naming of CH2 groups in pdb file

On 9/10/15 5:10 AM, Alex Cullen wrote: Dear Gromacs users, I have built a pdb file format for a polymer, and I want to use GROMOS FF. Therefore, I included polar Hydrogens in the pdb file, but I do not know how to name CH2 groups in NAME and SEGNAME columns. When executing the pdbtogmx command

[gmx-users] adding lipids

Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I don'

[gmx-users] adding lipids

Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I don'

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Hi again, Actually what I said is wrong. The right way to do it is: awk '{print $1, ($2<0) ? $2+360 : $2}' Sorry about that. On 10 September 2015 at 12:07, GAYATHRI S wrote: > Thank you very much. > That was helpful. > > Regards, > Gayathri S. > > > > > Hi, > > > > I'm assuming you are meas

[gmx-users] trajectory file (xtc) visualization by VMD

Hi guys! I have had a problem with VMD when reads frames on xtc file. It stops suddenly. It seemed VMD is working out of memory so I remove solvent molecules by trjconv command. It went further but still stops before the end. What should I do? Can I remove some frame from the beginning part? H​ow?

Re: [gmx-users] trajectory file (xtc) visualization by VMD

When you open the file you can set "first frame", "last frame"and "stride". Try to increase the stride to skip frames. On 10 September 2015 at 17:25, Homa rooz wrote: > Hi guys! > I have had a problem with VMD when reads frames on xtc file. It stops > suddenly. It seemed VMD is working out o

[gmx-users] GROMACS OPLS-AA question

Hello GROMACS users, I am interested in using the OPLS-AA as implemented in GROMACS. The OPLS-AA forcefield omits all nonbonded (Coulomb and LJ) interactions 1 and 2 bonds away. Nonbonded interactions 3 bonds are away are scaled by 1/2. Nonbonded interactions are applied without modification for a

[gmx-users] g_order

I have a molecule with a carbon chain attached to a ring. I want to use g_order to generate the ordering parameter across the simulation box. I've read the manual entry for g_order, and it said to create an index file with only the "relevant" atoms included, so I made a group with just the atoms in

[gmx-users] reaction field and permittivity

Dear Users, I used mdp file at the following url for NVE vacuum simulation http://shourjya.thinkbiosolution.com/wp-content/uploads/2013/02/nvevaccmdp1.txt Does epsilon_rf affect the simulation? epsilon_rf is dielectric constant beyond the cut-off. Since I set 0 for all the cut-off, the cut-off

Re: [gmx-users] reaction field and permittivity

On 9/10/15 4:40 PM, Johnny Lu wrote: Dear Users, I used mdp file at the following url for NVE vacuum simulation http://shourjya.thinkbiosolution.com/wp-content/uploads/2013/02/nvevaccmdp1.txt Does epsilon_rf affect the simulation? epsilon_rf is dielectric constant beyond the cut-off. No.

Re: [gmx-users] g_order

On 9/10/15 1:58 PM, Stella Nickerson wrote: I have a molecule with a carbon chain attached to a ring. I want to use g_order to generate the ordering parameter across the simulation box. I've read the manual entry for g_order, and it said to create an index file with only the "relevant" atoms in

[gmx-users] Creating a box of water with density 1000 g/l

Hi there, I am wondering if there is a better way to create a box with water of a certain size than: gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512 To get a density of roughly 1000 g/l i would need to add 512 molecules in such a box. But the script only adds 502. I co

Re: [gmx-users] Creating a box of water with density 1000 g/l

On 9/10/15 4:44 PM, Ebert Maximilian wrote: Hi there, I am wondering if there is a better way to create a box with water of a certain size than: gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512 To get a density of roughly 1000 g/l i would need to add 512 molecules in

Re: [gmx-users] Creating a box of water with density 1000 g/l

The reason is that I try to reproduce the experiment from the paper System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. before calculating the self diffusion coefficient for my organic solvent i wanted to see if

[gmx-users] oplsaa.ff parameters

Hello GROMACS users, oplsaa.ff/ffbonded.itp contains the following line: CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.0 0.0 ; hydrocarbon all-atom These values are at odds with those used provided in two publications listed in "oplsaa.ff/forcefield.it

Re: [gmx-users] Creating a box of water with density 1000 g/l

On 9/10/15 5:01 PM, Ebert Maximilian wrote: The reason is that I try to reproduce the experiment from the paper System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. before calculating the self diffusion coeffic

Re: [gmx-users] Creating a box of water with density 1000 g/l

I think I would do it this way. Use L that is slightly larger than 2.494 so that you can fit all of the 512 water molecules you want. Then run a very short simulation at 10 bar. The size of the box now should be less than 2.494. Now change the box size to 2.494 and then run the final equilibratio

[gmx-users] gromacs-5.1 with charmm36.ff

Hi I have run into a strange problem when making an urea+tip3p water box When trying to set up an energy minimization with gromacs-5.1 I get a grompp error: Program gmx grompp, VERSION 5.1 Source code file: /home/kuczera/prog/gromacs-5.1/src/gromacs/gmxpreprocess/toppush.c, line: 908 Fatal

Re: [gmx-users] gromacs-5.1 with charmm36.ff

On 9/10/15 6:17 PM, Krzysztof Kuczera wrote: Hi I have run into a strange problem when making an urea+tip3p water box When trying to set up an energy minimization with gromacs-5.1 I get a grompp error: Program gmx grompp, VERSION 5.1 Source code file: /home/kuczera/prog/gromacs-5.1/src/gromac

Re: [gmx-users] g_order

On 9/10/15 6:58 PM, Stella Nickerson wrote: I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against th

Re: [gmx-users] g_order

I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against the interface. I though Sz might illustrate that.

[gmx-users] NVE+NVE: Two groups: one with Tcouple while the other one not

Hi, I am modelling a box with two groups of molecule: N2 and C12H26. 1. Initially, NVT was used for both: ; Temperature coupling is on Tcoupl = nose-hoover tau_t = 1.0 1.0 tc-grps = N2 nC12 ref_t = 450 300 2. Then I turned off the Tcoupl for nC12 (by setting tau_t = -1): ; Temperatur

Re: [gmx-users] NVE+NVE: Two groups: one with Tcouple while the other one not

Sure. N2 heats the large moleculle which dissipates heat much more slowly and does not have a thermostat to help it. On Thu, Sep 10, 2015 at 9:09 PM, Guiyuan Mo wrote: > Hi, > > > I am modelling a box with two groups of molecule: N2 and C12H26. > 1. Initially, NVT was used for both: > > ; Te

Re: [gmx-users] NVE+NVE: Two groups: one with Tcouple while the other one not

The reason is the slow energy exchange between the gas and the solid. On Thu, Sep 10, 2015 at 9:47 PM, Guiyuan Mo wrote: > Okay. Thank you VV. > > But the simulation result show that the system temperature would go up to > 1000K after I turned off the Tcoupl for nC12 (by setting tau_t = -1). W

Re: [gmx-users] reaction field and permittivity

thank you very much. On Thu, Sep 10, 2015 at 4:43 PM, Justin Lemkul wrote: > > > On 9/10/15 4:40 PM, Johnny Lu wrote: > >> Dear Users, >> >> I used mdp file at the following url for NVE vacuum simulation >> >> http://shourjya.thinkbiosolution.com/wp-content/uploads/2013/02/nvevaccmdp1.txt >> >>

[gmx-users] How to create a spherocylindrical wall

Hi I would like to perform a simulation ( without any periodic boundary condition) where I need to have a wall of spherocylindrical geometry. In other words the particles will be confined inside a spherocylinder. Is there any good suggestion on how to achieve that in gromacs? 1) One option I t

[gmx-users] g_hbond

Dear all I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file. Then with xpm2ps I converted .xpm to .eps file. I get half the number of rows in .eps file as compared to .ndx file. when using Justins perl script I got summary of existence file and here 12 bonds are shown but in .ep