[gmx-users] on g_rms analysis

Dear All,   Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to 3 ns, will you please tell me the corresponding g_rms command?   Cheers,   Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

Re: [gmx-users] on g_rms analysis

On 10/04/2012 4:59 PM, Acoot Brett wrote: Dear All, Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to 3 ns, will you please tell me the corresponding g_rms command? g_rms has options that allow you to select the start and finish time for the analysis. Look them u

Re: [gmx-users] SS bond forcing

Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index typ

[gmx-users] Problem with g_dipoles and SPCE water

Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Groma

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the com

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and rep

[gmx-users] martini coarse-grained

Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .it

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin, Could you tell me for what purposes the definition of the several ref_t values could be usefull? Does this just for measurements of the temperature during simulation for each group separately or is there something else? By the way as I've found in literature another important question ab

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 04/10/2012 11:10 AM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: > On 2012-04-10 09:43, Tom Kirchner wrote: >> Hi all, >> >> I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E >> water. Sadly the result for the dielectric con

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 2012-04-10 11:16, Tom Kirchner wrote: On 04/10/2012 11:10 AM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: > On 2012-04-10 09:43, Tom Kirchner wrote: >> Hi all, >> >> I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E >> wate

[gmx-users] Error: 4095 characters, fgets2 has size 4095

Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has siz

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: > Dear Gmx Users, > > It is 1st time I came across such problem. While preparing my

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

Thank you for the reply. I do not have such files in my directory or in my force field. On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner wrote: > Hi Steven, > > you might have to remove files with weird names (such as ._name) in the > directory where you run > grompp or in your forcefield direc

[gmx-users] Gromacs on "HPC workstations" ?

Hi, I'm currently looking for hardware solutions to run MDs and would like to benefit from your experience concerning the hardware. It would mainly be simulations in the range of several thousands of CPU hours, and occasionally for hundreds of K hours (paralleled on 64 to 256 nodes max). There'

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

On 2012-04-10 12:02, Steven Neumann wrote: Thank you for the reply. I do not have such files in my directory or in my force field. did you mean dos2unix? try: wc grompp.mdp to count the number of lines. There should be may. In fact grompp probably tells you which input file is erroneous, doesn'

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel wrote: > On 2012-04-10 12:02, Steven Neumann wrote: > >> Thank you for the reply. I do not have such files in my directory or in >> my force field. >> > did you mean dos2unix? > > try: > wc grompp.mdp > to count the number of lines. There shoul

Re: [gmx-users] SS bond forcing

pitheve...@free.fr wrote: Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restr

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

On 2012-04-10 12:38, Steven Neumann wrote: On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: On 2012-04-10 12:02, Steven Neumann wrote: Thank you for the reply. I do not have such files in my directory or in my force field.

Re: [gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file?

Hi Catherine, A converged system will yield low cosine content. But that can't be turned around! I can think of a lot of lines that don't match well with a cosine, but that are inconsistent with convergence. That said, the index in the .xvg file is the principal component index. So the projection

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: Justin, Could you tell me for what purposes the definition of the several ref_t values could be usefull? Does this just for measurements of the temperature during simulation for each group separately or is there something else? Each ref_t value is the target tempe

Re: [gmx-users] martini coarse-grained

Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C- C. Is it

Re: [gmx-users] SS bond forcing

How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it. Thank you -- Pierre THEVENET Ph.D. Can

Re: [gmx-users] SS bond forcing

Pierre THEVENET wrote: How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it. I can't predict how much time it

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul написал: > > I have never used the bd integrator so I cannot offer any help here. I > don't see any magical reason why you should expect it to enhance sampling > though. I've found in the literature that this integrator could rise

[gmx-users] on 2 different mini.mdp file

Dear All,   The first mini.mdp is as following:   ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Sto

Re: [gmx-users] SS bond forcing

In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max) -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole D

[gmx-users] lipid.itp for AMBER-GAFF

Hello, I am following the 'KALP15 in DPPC tutorial' but using GAFF with DOPC (from http://lipidbook.bioch.ox.ac.uk/package/show/id/32.html) and my membrane protein. Is there an equivalent file to lipid.itp for AMBER-GAFF? Kind regards, Henry --

[gmx-users] Can gromacs handle reflective boundary condition ?

Dear, Can gromacs handle reflective boundary condition, in order to remove the periodicity of Z-axis ? Do I need to take advantage of walls and Ewald ? Thanks so much! You

Re: [gmx-users] lipid.itp for AMBER-GAFF

Henry Hocking wrote: Hello, I am following the 'KALP15 in DPPC tutorial' but using GAFF with DOPC (from http://lipidbook.bioch.ox.ac.uk/package/show/id/32.html) and my membrane protein. Is there an equivalent file to lipid.itp for AMBER-GAFF? There is a lipid force field that has been

[gmx-users] Structures and topologies of cholesterol-containing membranes

Hi, we have recently put a website online with structures and topologies of a large set of 28 different cholesterol-containing membranes: http://cmb.bio.uni-goettingen.de/cholmembranes.html Structures of membranes containing - DMPC - DPPC - POPC - DOPC - POPE - POPE and POPC plus different

Re: [gmx-users] SS bond forcing

Pierre THEVENET wrote: In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max) Well, if you try the distance restraint approach,

Re: [gmx-users] on 2 different mini.mdp file

Acoot Brett wrote: Dear All, The first mini.mdp is as following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul > написал: I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance sampling though. I

Re: [gmx-users] SS bond forcing

Ok. Thank you for your help. I will try to do it and see if it not too time consuming. -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul > > > Pierre THEVENET wrote: > >> In most cases (

[gmx-users] protein folding / pbc

Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to

Re: [gmx-users] protein folding / pbc

On 11/04/2012 1:24 AM, Shi, Huilin wrote: Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the

[gmx-users] multiple dihedral function types - regd

Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two

RE: [gmx-users] protein folding / pbc

So if I wanna run a simulation to unfold the protein, I need make a big box that is large enough so that the unfolded protein is still smaller than the box in any dimension. Is this correct? Thanks. Huilin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@g

Re: [gmx-users] Box generation for monoclinic crystal - regd

Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608

Re: [gmx-users] protein folding / pbc

Correct. On Tue, Apr 10, 2012 at 1:22 PM, Shi, Huilin wrote: > So if I wanna run a simulation to unfold the protein, I need make a big box > that is large enough so that the unfolded protein is still smaller than the > box in any dimension. Is this correct? > > Thanks. > > Huilin > __

[gmx-users] martini coarse-grained

- Forwarded Message - From: dina dusti To: XAvier Periole Sent: Tuesday, April 10, 2012 10:44 PM Subject: martini coarse-grained Thank you very much from your response. I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of mo

Re: [gmx-users] Box generation for monoclinic crystal - regd

Hi Ramesh, Maybe it is easier, and less error-prone, to work in PDB format, specifying the box as a CRYST1 record. You can use the PDB format anywhere in your workflow where GRO format is used. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla wrote: > Dear Mark, > >

Re: [gmx-users] martini coarse-grained

Hi Dina, Thiophen is a five-membered ring, like the histidine side-chain, which is modeled with three beads. And then you ought to choose the bead types such that they give good agreement with atomistic PMFs and/or partitioning of the same compound. It's very unlikely that just fiddling around a b

Re: [gmx-users] Box generation for monoclinic crystal - regd

Dear Tsjerk, Thank you for your reply, I will try to work with PDB format and get back to you. On Wed, Apr 11, 2012 at 12:22 AM, Tsjerk Wassenaar wrote: > Hi Ramesh, > > Maybe it is easier, and less error-prone, to work in PDB format, > specifying the box as a CRYST1 record. You can use the PDB

[gmx-users] Particle Insertion with Buckingham Potential

I switched the potential calculation from Lennard-Jones to Buckingham. After the switch, the simulations that I submit encounter the following error: Fatal error: Not enough memory. Failed to realloc 2812110160 byes for *bin, *bin=0x83fd1008 (called from file tpi.c, line 109). I find this puzzlin

Re: [gmx-users] Box generation for monoclinic crystal - regd

On 11/04/2012 4:13 AM, ramesh cheerla wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.

[gmx-users] martini coarse-grained

Hi Tsjerk, Thank you very much from your response. OK, it means that I should select SC4, SC4 and SC5 for tiophen (SC4s = C-C and SC5 = S)? On the other hand, I have 2 other structure, aniline and pyrrole. If I select three beads for both of them consist of SC4, SC4 and SP1, consequently, they

Re: [gmx-users] multiple dihedral function types - regd

On 11/04/2012 3:33 AM, ramesh cheerla wrote: Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology f

Re: [gmx-users] Can gromacs handle reflective boundary condition ?

On 10/04/2012 11:50 PM, stjohn55 wrote: Dear, Can gromacs handle reflective boundary condition, in order to remove the periodicity of Z-axis ? No. Mark Do I need to take advantage of walls and Ewald ? Thanks so much!

Re: [gmx-users] multiple dihedral function types - regd

Thank you mark. On Wed, Apr 11, 2012 at 8:09 AM, Mark Abraham wrote: > On 11/04/2012 3:33 AM, ramesh cheerla wrote: > >> Dear gromacs users, >> >> For one of my residues i have two types of >> dihedral functions, i.e C-C dihedrals are in periodic type and C-O >>

Re: [gmx-users] Box generation for monoclinic crystal - regd

Thank you mark. On Wed, Apr 11, 2012 at 6:15 AM, Mark Abraham wrote: > On 11/04/2012 4:13 AM, ramesh cheerla wrote: > > Dear Mark, > > Thank you for reply, sorry for not being very clear, Here my > doubt is can i use triclinic box for the simulations of the crystal whose > unit c

[gmx-users] regarding micelle and its analysis

hello sir, i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles. my doubt is while performing analysis , g_gyrate giving a value of around 3nm.. this value corresponds to which micelle.. how its ca