[gmx-users] what does the Coulomb (SR) mean under PME?

Hi all, Anybody can help me out! Thanks in advance? In my test simulation, there are one Na^+ and one Cl^- (the distance of 1nm) in vacuum in a very big simulation box (10*10*10 nm^3). I calculated the energies under two different conditions, coulombtype=PME vs coulombtype=cut-off. 1.

[gmx-users] Re: implicit wall doesn't recognize the wall_atomtype correctly?

Hi, Firstly, regarding my last email, even though I didn't get any complain about the nonsense setting for the wall_atomtype from grompp, the mdrun is crashed after some steps. Then I tested some atomtypes which have been given in OPLS, and checked the output in md.log: a) When wall_atomtype =

[gmx-users] Specified frame doesn't exist or file not seekable when using .xtc

Hi, all When I using the .xtc file to analyse, I always meet the following error information Specified frame doesn't exist or file not seekable While it works when using the .trr file. In analyzing, only the coordinate is used. Therefore, I want to use .xtc file. In this way, it runs a little

Re: [gmx-users] Specified frame doesn't exist or file not seekable when using .xtc

, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi, all When I using the .xtc file to analyse, I always meet the following error information Specified frame doesn't exist or file not seekable While it works when using the .trr file. In analyzing, only the coordinate

[gmx-users] question about the total-energy of energy minimization

Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 - 919.923 Coulomb-(SR) -35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.1

Re: [gmx-users] g_sdf again

2007/3/29, Dallas B. Warren [EMAIL PROTECTED]: Syma, I am using g_sdf to calculating the spatial distribution of lipid headgroups around other species in my system. The thing is when I get the gro file (produced by using the -r flag in g_sdf) and then look at this in vmd or chimera with

Re: [gmx-users] g_rdf normalisation

2007/3/26, syma [EMAIL PROTECTED]: Hi, I am attempting to calculate the rdfs of the various components of my system wrt to DNA phosphate groups. However, I was wondering how I can normalise so I can compare the various rdfs? Ideally I would like to have the g(r) normalised in the range 0-1.

Re: [gmx-users] coordination number of ion: rdf integration

2007/3/16, [EMAIL PROTECTED] [EMAIL PROTECTED]: Hi all, I am struggling with the rdf. I have 7 structural ions in my protein and I'd like to monitor the coordination number around them (ion - protein) during my MD. I have read papers about it and:

Re: [gmx-users] coordination number of ion: rdf integration

2007/3/16, andrea spitaleri [EMAIL PROTECTED]: Qiao Baofu wrote: When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr]. fine. this is clear, where rho = N/V and N = number of particles (7 ions in this case) and V is the total Volume. N is the total number of the atoms

Re: [gmx-users] How to calculate angle dependent rdf

Do you mean SDF, which has been implement by different workers? Or you can rewrite it according to your aim. 2007/3/12, 齐文鹏 [EMAIL PROTECTED]: Dear everyone, I read it from the 3.3 manual that the g_rdf program can calculate the angle dependent rdf. But I cannot find how to implement it ?

Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation

2007/3/8, Itamar Kass [EMAIL PROTECTED]: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using

Re: [gmx-users] positive system total-energy

159.458 0.0103536 103.395 Temperature 399.9283.172723.17272 2.21097e-07 0.00220797 2007/3/6, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi, I have a 10 ns job. But when using the g_energy to calculate the component of the energy, I got a positive total-energy

Re: [gmx-users] g_rdf

2007/3/7, marco cammarata [EMAIL PROTECTED]: Hi, I'm using g_rdf to calculate the RDF of a system. The r range ends at 3nm. r range ends at 3nm because (your box size)/2 is 3 nm I would like to change it to 100nm but it seems that there are no option for it. 100 nm? Are you sure? it

Re: [gmx-users] Protein Dipole moment

no. the com is not used in the g_dipoles. The simplest way to use com is to replace the content of the { void mol_dip() } with the following code. int k,kk,l; real q,m,m_sum,q_sum; q_sum = 0; m_sum = 0; for(k=k0; (kk1); k++) { kk = ma[k]; q_sum

[gmx-users] positive system total-energy

Hi, I have a 10 ns job. But when using the g_energy to calculate the component of the energy, I got a positive total-energy!! Who can give some suggestions? Thanks a lot! The NTP ensemble is used. Before the final run, it has been run for 2ns to get the equilibrium state. The system has

[gmx-users] question about genbox -vdwd

Hi all, I have one question: when I use the genbox -nmol 300 -ci a.gro -cp b.gro to insert a.gro into b.gro, for some system it gives good results, while not for others. On the other hand, the -vdwd opinion seems not work. I looked at the code of gmx_genbox.c, but didn't find the reason. From

Re: [gmx-users] Re: fudgeQQ (again ...) and fudgeLJ

Hi, I have just tested the fudgeQQ and fudgeLJ, and found one problem: I use the ffoplsaa force field, and add the atoms I used.(in the ffolpsaanb.itp file, there is no [pairtype] section, and I only add the atom informations: ; name bond_typemasscharge ptype sigma

Re: [gmx-users] Re: fudgeQQ (again ...)

2006/12/7, [EMAIL PROTECTED] [EMAIL PROTECTED]: By the way, why are you using the combination of genpairs=yes fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for any force field that comes in the standard gromacs distribution. Hi, I am puzzled about this. In your opinion,

[gmx-users] strange NTP trajectory

Hi all, I run NTV firstly for 100ps, then change to NTP for 1ns. The mdrun finished with the common informations. But when I use vmd (or ngmx) to look at the trajectory, I found that during the NTP stage, starting from 100ps, all the molecules don't move except only one molecules. The output

[gmx-users] How to get a equilibriumed system effectively

Hi all, Now I meet a problem when building a system. I used prodrg to get the .pdb of a single molecule, write the .top file manually. The single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for at least 1 ns). Then I used two method to get a bigger (8 molecules) system: 1)

Re: [gmx-users] how to simulate at a specific dielectric constant

Hi David,There is not a simulation parameter that you can change that will influence the dielectric constant of your system. I don't grasp this. If the system has two fluid, one as solute, another as solvent. I had thought that I should change the value epsilon_r in the .mdp file from the default

Re: [gmx-users] how to simulate at a specific dielectric constant

yes. In the .mdp, epsilon_r gives the relative permittivity of the medium2006/11/15, Mark Abraham [EMAIL PROTECTED]: Dear allHow can i set the dielectric constant of my choice in the simulationsPlease read the manual.Mark ___ gmx-users mailing list

[gmx-users] calculating dielectric constant

Hi all,I have some question about calculating dielectric constant:1. From the manual, it seems that there are two methods to calculate the dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use g_dipoles -nonormalize -corr total -c dipcorr.xvg, then g_dielectric -f dipcorr.xvg -o

Re: [gmx-users] calculating dielectric constant

are the values what I expect. What wrong?2006/11/13, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi all, I have some question about calculating dielectric constant: 1. From the manual, it seems that there are two methods to calculate the dielectric constant: a. use g_dipoles -temp 400 -f -s

Re: [gmx-users] question about energy fluctuation

-10.6792 -5339.61Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99 2006/11/9, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981

[gmx-users] question about energy fluctuation

Hi all,After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy:*Last frame read 1557952 time 1557.952Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2

Re: [gmx-users] question about energy fluctuation

Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules.I am using Gromacs 3.3.1. You can divide by the

[gmx-users] problem in compiling g_velacc again under gromacs

Hi all,I want to comile the g_velacc again. I copy the original gmx_velacc.c and autocorr.c into a new directory, and then comile the gmx_velacc.c, but it gives the following complains, and then exits. (I didn't change anything in the two files!!) How to solve it? Thanks a lot.

Re: [gmx-users] problem in compiling g_velacc again under gromacs

to 64-bite system. /usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when searching for -lmd/usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when searching for -lmd/usr/bin/ld: cannot find -lmd collect2: ld returned 1 exit status2006/10/31, Qiao Baofu [EMAIL

[gmx-users] question about calculation electrical conductivity with green-kubo relation

Hi all,I wrote a program to calculate the electrical conductivity at zero field using the Green-Kubo relation, as follows. But I found the calculated data are strange: in the first stage, the data are very big, while in the end stage it is a negative value, also quite big. (I used the system with

Re: [gmx-users] strange new H-H bond formation during MD

Thanks.I check the animation of VMD again, and found that during the animation, some H-H connections are displayed. But as the time grow, they disappear sooner or later. On the other hand, the mdrun didn't crash for 500 ps ( 0.001ps/step). Therefore, I think it is the problem of the display of

Re: [gmx-users] strange new H-H bond formation during MD

Yes. Gromacs can only generate the .pdb file without CONNECTION. I think it is not only Gromacs but Material Studio that do like that. For more than 2 molecules, the softwares give only the coordinate data. I find a top2psf.tcl file on the website of VMD (Script Library). It is said this script

Re: [gmx-users] strange new H-H bond formation during MD

Hi Tsjerk,Yes, you are right!2006/10/24, Tsjerk Wassenaar [EMAIL PROTECTED]: Note that it should be CONECT and not CONNECT...Tsjerk-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main,

[gmx-users] strange new H-H bond formation during MD

Hi All,I meet a problem in run MD: from the display of VMD, there are some H-H bonds formed during the MD. All the bonds I wrote in .itp file are right, except these new unexpected H-H bonds. (I generate the system from a smaller system, EM is ok, when running NTV, the problem comes. ) Who can

Re: [gmx-users] strange new H-H bond formation during MD

Thanks. Now I understand what happens.But in the user-manual of VMD, it is said that only four Gromacs file (GRO, G96, XTC, TRR) and .pdb can be read by VMD. But only the .pdb contain the information of bond-connectivity (if I understand correctly). The point is that the output .pdb file from

[gmx-users] warning: assignment makes pointer from integer without a cast

Hi all,I meet a problem in compiling my program under gromacs: it always give the information warning: assignment makes pointer from integer without a cast. The line refers to the following line with (***). I have tried opt2fn_NULL too. How to solve it? and can you give some introduction about

[gmx-users] calcualting viscosity from NEMD

Hi all,I want to calculate the shear viscosity of a small molecule pure fluid. Therefore, I run some non-equilibrate MD. But I don't know what values should be given to accelerate and cos-acceleration. Please see my results below. I found that:1. with the cos-acceleration decreasing, 1/viscosity

Re: [gmx-users] question about energy and pressure

Hi Mark,2006/9/22, Mark Abraham [EMAIL PROTECTED]: Qiao Baofu wrote:What is this reported data?The reported data are (KJ/mol) : Bond 27; Angle: 30; LJ: -27; electrostatic -530.Some days ago, I run again in gromacs but using all the reported force-field parameters. In the end, I get the similar

[gmx-users] question about energy and pressure

Hi all,I have some questions about the gromacs:1. I simualted a pure small molecule system. All the simulation is ok. But when I use g_energy to calculate the energy of bond, angle, lj, and coloumb, it gives the following energy. The energies is much bigger, about 50-100 times bigger than the

Re: [gmx-users] 1-4 columb interaction

In the force field file ff***.itp, there are two terms to scale lj and coloumb after the option: generating pairs.2006/9/20, Alok [EMAIL PROTECTED] : Dear All, Is thereany scaling for 1-4 columb interaction in gromacs force field if yes then how? is it also like LJ14 which uses separate

[gmx-users] Re: question about g_rdf -com a little mistake on make_ndx

3Splitting group 3 'MIL' into residues2006/9/15, Qiao Baofu [EMAIL PROTECTED]:Hi AllI have 2 questions about using g_rdf -com: 1. In the manual, it is said that when -com option used, the rdf is calculated with respect to the center of first group. My question is that, if i want to calculate the rdf

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

Hi,Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ; MD steps 4

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006/9/14, Mark Abraham [EMAIL PROTECTED]: Probably your interconnects between nodes are using carrier pigeons orsomething :-) I expect that 1 cpu on machine A will require around fourtimes as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to run only one cpu on

Re: [gmx-users] how to write a annealing .mdp

Hi, set T_couple=no and refer to the following script; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic)annealing = single; Number of time points to use for specifying annealing in each group annealing_npoints = 6; List of times at the annealing points for

Re: [gmx-users] Question about angle constraints

to be included#include ffoplsaa.itp; include the PF6- topology#include PFN.itp[ system ]PFN[ molecules ]; molecule name number PFN 52006/8/30, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi All, In my simulation, the NO3- is used, in which the three

[gmx-users] Question about angle constraints

Hi All,In my simulation, the NO3- is used, in which the three N-O bond length is constraints. And a planar triangular structure is used. I used the type 1 of [ constraints ] to constraint the bond length. Because I only find angle constraints which is used on H-involved angles, I used the type 2