[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. "coulom

[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 = o

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 w

[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 fas

[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 -46818.120524

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

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, 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

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: http://www.gromacs.org/pipermail/gmx-users/200

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 P

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?

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

79.2162.228159.458 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 > componen

[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 about

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; (k: Hello Does g_dipole take the cen

[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] loss of information trr xtc

If I understand correctly, only the coordinate information can be saved in .xtc. That means, all other informations, velocity, force, etc, can't be reconverted into .trr again. 2007/2/9, Joern Lenz <[EMAIL PROTECTED]>: hi guys. can anyone tell me if there is a loss of information when i conve

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 ep

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 file

[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) ge

Re: [gmx-users] radial distribution function

To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of group B to get the gAB(r). g_rdf -com calculate the center of group A, not the centers of the residues in group A to all the atoms of group B. I upload a file based on gmx_rdf.c to calculate the centers of residues of g

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 1

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 all>  How can i set the dielectric constant of my choice in the simulationsPlease read the manual.Mark ___ gmx-users mailing list

Re: [gmx-users] calculating dielectric constant

ilon = -2.01094 _Neither result 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 se

[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] question about energy fluctuation

0.588   -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 gives the

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 num

[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 data

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

Hi,I compile it again in the source folder   ~/src/tool/ and the installation folder  ~/gromacs/bin.  It give the same complains.What can I do?2006/10/31, Mark Abraham < [EMAIL PROTECTED]>:Qiao Baofu wrote: > Hi all,>> I want to comile the g_velacc again. I copy the original  gm

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

[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. **

[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 a

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 VMD.

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, G

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 ca

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 mdru

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

Hi Mark,Thanks for your reply.I used these:   1. vmd em_out.gro    2. use the "load data into molecules...", select md1.trr, and then load  3. when the anmination is finished, I can see some H-H bonds. 2006/10/23, Mark Abraham <[EMAIL PROTECTED]>: > Hi All,>> I meet a problem in run MD: from the di

[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 g

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

Hi David,Thanks a lot.Now, it works.2006/10/19, David van der Spoel <[EMAIL PROTECTED]>: Qiao Baofu wrote:> 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 cas

[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 t

[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/visc

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 par

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

Hi Dallas Warren,1. The molecules are the same. But we built the system in different method, and used different number of molecules. 2. We both used the oplsaa all-atom force field, but the parameters are a little different. 3. I used gromacs. The reference used MDynaMix.4. The unit of energy are

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 there any scaling for 1-4 columb interaction in gromacs force field if yes then how? is it also like LJ14 which uses separa

[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 repor

[gmx-users] Gromacs install question

Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configu

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

x27;MIL' into atoms> splitat 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

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 o

Re: [gmx-users] Re: Re: Re: Question about parallazing Gromacs

Thanks a lot!2006/9/14, Cesar Araujo <[EMAIL PROTECTED]>: > -->> Message: 7> Date: Thu, 14 Sep 2006 09:27:45 +0200> From: "Qiao Baofu" <[EMAIL PROTECTED]>> Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao &g

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 s

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 a

[gmx-users] Question about parallazing Gromacs

Hi all,I have a question about parallazing gromacs: I run the same system on a cluster of my institute and my local computer,     Cluster: dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz     Local computer: AMD X86-64 Cpu, double precision1. The cluster (nodes=3:ppn=4) runs  87950 MD st

Re: [gmx-users] Question about angle constraints

2006/8/30, David van der Spoel <[EMAIL PROTECTED]>: Qiao Baofu wrote:> 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 con

[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 "