Re: [gmx-users] Linear CG beads, grompp doesn't work

2013-01-02 Thread XAvier Periole
I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. As far as I know angles have never made martini unstable but the conventi

[gmx-users] genbox did not run?

2013-01-02 Thread Mijiddorj
I am a new user of Gromacs, I have problem with genbox. When I run genbox following error occurred:Program genbox, VERSION 4.5.5Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and tip

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
Justin, I've already tried use g_x2top for the model of the system built from regularly spaced C-atoms ( with included hydrogens to specify sp3 hybridization). By means of that command I've created topology for my lattice with big force constant ( for the simulation of the very rigid structure)

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 4:36 AM, James Starlight wrote: Justin, I've already tried use g_x2top for the model of the system built from regularly spaced C-atoms ( with included hydrogens to specify sp3 hybridization). By means of that command I've created topology for my lattice with big force constant ( fo

Re: [gmx-users] genbox did not run?

2013-01-02 Thread Justin Lemkul
On 1/2/13 4:20 AM, Mijiddorj wrote: I am a new user of Gromacs, I have problem with genbox. When I run genbox following error occurred:Program genbox, VERSION 4.5.5Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output error:/home/mijiddorj/Desktop/Tutorial

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
Justin, so why my simulation of the sp3 lattice have been crashed with the links warnings ( which always tells about wrong geometry in topology)? also I've tried to paraetrize completely planar (sp2) lattice but obtain errors like that Can not find forcefield for atom C27-22 with 2 bonds Can not

Re: [gmx-users] dodecahedron box

2013-01-02 Thread Justin Lemkul
On 1/2/13 7:03 AM, Turgay Cakmak wrote: Dear gromacs users, I am trying to solvate several peptides (at a desired positions) in a dodecahedron box. I have done following steps; 1) editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp peptides_nb.gro

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 7:15 AM, James Starlight wrote: Justin, so why my simulation of the sp3 lattice have been crashed with the links warnings ( which always tells about wrong geometry in topology)? Incorrect geometry is not the only cause of LINCS warnings. I haven't seen nearly enough information

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Bogdan Costescu
On Wed, Jan 2, 2013 at 1:15 PM, James Starlight wrote: > so why my simulation of the sp3 lattice have been crashed with the > links warnings ( which always tells about wrong geometry in topology)? I might have missed something from the beginning of this discussion... Why do you use LINCS with a l

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
Bogdan, Thank you for explanation. Indeed the problem was in the LINCS constrains which was not required for the lattice system. By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydrogens atoms only ( only atoms forming lattice sca

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
by the way also I'd like to know what options for the pbc should I specify that my system looked like infinite lattice in the x-y dims ? James 2013/1/2, James Starlight : > Bogdan, > > Thank you for explanation. Indeed the problem was in the LINCS > constrains which was not required for the latti

[gmx-users] Re: genbox did not run?

2013-01-02 Thread Mijiddorj
Thank you, I got it. Mijiddorj -- View this message in context: http://gromacs.5086.n6.nabble.com/genbox-did-not-run-tp5004186p5004197.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] grompp error

2013-01-02 Thread Mijiddorj
Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshooting, please check the GROMACSwebsite at htt

Re: [gmx-users] grompp error

2013-01-02 Thread Justin Lemkul
On 1/2/13 10:01 AM, Mijiddorj wrote: Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshootin

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 8:58 AM, James Starlight wrote: Bogdan, Thank you for explanation. Indeed the problem was in the LINCS constrains which was not required for the lattice system. By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydroge

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 9:26 AM, James Starlight wrote: by the way also I'd like to know what options for the pbc should I specify that my system looked like infinite lattice in the x-y dims ? Do you want the lattice to be infinite or do you just want it to look like it's infinite? If you want an infini

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Bogdan Costescu
On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote: > By the way now I'd like to simulate the same 2D flexible ( in non > planar hybridization) lattice but consist of non-hydrogens atoms only > ( only atoms forming lattice scaffold ). Does it possible to change > Carbon atom-valence (from 4 to

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 10:14 AM, Bogdan Costescu wrote: On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote: By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydrogens atoms only ( only atoms forming lattice scaffold ). Does it possible t

[gmx-users] Re: grompp error

2013-01-02 Thread Mijiddorj
Dear Justin, Thank you for your helpful suggestion. Mijiddorj From: Justin Lemkul [via GROMACS] To: Mijiddorj Sent: Wednesday, January 2, 2013 11:10 PM Subject: Re: grompp error On 1/2/13 10:01 AM, Mijiddorj wrote: > Hello all, I am new user of groma

[gmx-users] Phosphorylation

2013-01-02 Thread Алексей Раевский
Hi, all. Does anybody know wether I have to put a phosphorylated residue in the kinase's activation loop (last example is pdbid 2Y94) or not, when I'm working with protein-inhibitor complex without any type of protein-protein interactions? Or it is necessary only when I'm working with p-p complexes

[gmx-users] Amidated C-terminal

2013-01-02 Thread Shima Arasteh
 Hi, In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and then getting top file, when I see the top file,

Re: [gmx-users] Amidated C-terminal

2013-01-02 Thread Justin Lemkul
On 1/2/13 2:07 PM, Shima Arasteh wrote: Hi, In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and th

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
Justin, I want to simulate flexible lattice consist of only one type of atoms (nodes). So the planar (sp2 ) carbons are rigid. On other hand more flexible (sp3) carbons connected with hydrogens but I want that hydrogens were not included in my lattice. Should I use another (what? )atom-type for t

[gmx-users] MPI segmentation Fault

2013-01-02 Thread Xu Dong Huang
Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will gener

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Xu Dong Huang
Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the stru

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread Justin Lemkul
On 1/2/13 3:08 PM, James Starlight wrote: Justin, I want to simulate flexible lattice consist of only one type of atoms (nodes). So the planar (sp2 ) carbons are rigid. On other hand more flexible (sp3) carbons connected with hydrogens but I want that hydrogens were not included in my lattice

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Justin Lemkul
On 1/2/13 3:20 PM, Xu Dong Huang wrote: Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Sh

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Xu Dong Huang
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run For NVT.mdp: integrator = md tinit= 0.0 dt = 0.02 nsteps = 1 nstcomm = 1 comm-grps

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Xu Dong Huang
@Justin, forgot to mention, yes the NVT was ran using MPI as well. (You're right, the MPI is not the issue, because I took the file off my cluster and attempted to run NPT on my personal computer, it reported same segmentation error, fault 11) Xu Dong Huang Chemical & Biochemical Engineering Ru

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Justin Lemkul
On 1/2/13 3:42 PM, Xu Dong Huang wrote: @Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run For NVT.mdp: integrator = md tinit= 0.0 dt = 0.02 nsteps = 10

Re: [gmx-users] MPI segmentation Fault

2013-01-02 Thread Xu Dong Huang
Dear Justin, I will try your suggestion to rerun it on Berendsen coupling and see if there is any further problems. The system indeed contain the star shaped structure I showed you earlier (running multiple versions, containing from 1, 5, 10, 15 and 20 stars in a solvent box), the solvent is ju

Re: [gmx-users] Amidated C-terminal

2013-01-02 Thread Shima Arasteh
The version of GROMACS I'm using is 4.5.5. I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl C. Is there any problem with the C36 which I use? [ SER ]  [ atoms ]     N    NH1    -0.47    0     HN    H    0.31    1     CA    CT1    0.07    2     HA    HB    0.09  

Fw: [gmx-users] Amidated C-terminal

2013-01-02 Thread Shima Arasteh
The version of GROMACS I'm using is 4.5.5. I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl C. Is there any problem with the C36 which I use? [ SER ]  [ atoms ]     N    NH1    -0.47    0     HN    H    0.31    1     CA    CT1    0.07    2     HA    HB    0.0

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-02 Thread James Starlight
Justin, I want to simulate lattice with flexible nodes ( to examine fluctuations of that system by mens of Normal Mode Analysis). If I choose sp3 carbons as the nodes I obtain such lattice. But In that system hydrogens are also present which are not desirable in my system ( i want system consiste