RE: [gmx-users] PME problem on BG/P cluster

----- From: LuLanyuan Date: Wednesday, June 9, 2010 2:10 Subject: RE: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org > Dear Mark, > When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any > problem. So I guess it's related to the assembly l

RE: [gmx-users] PME problem on BG/P cluster

] PME problem on BG/P cluster - Original Message - From: LuLanyuan Date: Saturday, June 5, 2010 2:01 Subject: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org > Hello, > I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" >

RE: [gmx-users] PME problem on BG/P cluster

roblem on BG/P cluster > > On 2010-06-04 17.49, LuLanyuan wrote: > > Hello, > > I got a weird problem by running Gromacs 4.0.7 on a BG/P machine > > ("Intrepid" at Argonne national lab). > > The simulated system is a box of SPC water with 648,000 atoms a

[gmx-users] PME problem on BG/P cluster

Hello, I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at Argonne national lab). The simulated system is a box of SPC water with 648,000 atoms and all MD simulations were performed on 256 CPU cores with MPI. The compiling environment was Linux with IBM compiler and

RE: [gmx-users] question about all atoms lipid molecule structure and force field

Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and

[gmx-users] weird tabulated potential problem

Hi, Some months ago I reported a strange conflict between the GMX 4 new option nblist=-1 and tabulated potentials. At that time I contacted Berk and he could run my test system without any problem. So I thought I had something wrong for my system configurations. However, recently I re-checked t

RE: [gmx-users] interpolation for tabulated potential

I saw it. Thanks. Lanyuan > Date: Wed, 14 Oct 2009 14:50:02 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] interpolation for tabulated potential > > LuLanyuan wrote: > > Hello, > > I'm just wondering what i

[gmx-users] interpolation for tabulated potential

Hello, I'm just wondering what interpolation method is used for the tabulated potential function in GMX. Since GMX 4, the input table contains potential and force, unlike potential and second derivative in GMX 3. Is cubic spline still used in GMX 4? If yes, what algorithm is implemented to get

RE: [gmx-users] user defined potential function for 1-4 interaction

Hi, As I remember, you can only use one table for 1-4 interactions. Don't know if it's changed in the latest version. Lanyuan > From: mhrah...@dal.ca > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] user defined potential function for 1-4 interaction > Date: Thu, 8 Oct 2009 19:10:39 -0300

RE: [gmx-users] A question regarding single sum virial

kker/ > > Cheers, > > Tsjerk > > 2009/8/12 LuLanyuan : > > Hello all, > > I got a question when I read the the manual chapter for the single sum > > virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't > > delta here also depend on in

RE: [gmx-users] A question regarding single sum virial

Henk Bekkers PhD thesis, available > at: > http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/ > > Cheers, > > Tsjerk > > 2009/8/12 LuLanyuan : > > Hello all, > > I got a question when I read the the manual chapter for the single sum > &g

[gmx-users] A question regarding single sum virial

Hello all, I got a question when I read the the manual chapter for the single sum virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here also depend on index j? I think delta is zero when particle i and j are close. And delta can be something else when any x/y/z c

[gmx-users] Wrong pressure with "mdrun -rerun" option

Hello all, >From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be >correct. However, I did a test for a box of tip3p water and found the pressure >results from rerun were different compared to the original results. For the >first MD simulation , I simulated it for 200 ps

RE: [gmx-users] What's the max number of pull groups?

Thanks so much, Berk. I have another question regarding the pull code. Can I define a pull group that contains more than one molecules? I tried to define some lipid molecules as a single pull group and pull them out of a bilayer. But I couldn't see the lipids out. If I try one lipid as a pull g

[gmx-users] What's the max number of pull groups?

Hello, Could anyone tell me what the maximum number of COM pulling groups is in GMX 4? Thanks very much. Lanyuan Lu _ MSN 表情魔法书，改变你的对话时代！ http://im.live.cn/emoticons/___ gmx-users mailing

RE: [gmx-users] A question regarding the xdr lib

Thanks very much, David. Lanyuan > Date: Mon, 6 Apr 2009 22:56:43 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] A question regarding the xdr lib > > LuLanyuan wrote: > > Hello, > > I just compiled the xdr file lib tha

[gmx-users] A question regarding the xdr lib

Hello, I just compiled the xdr file lib that was recently released on the Gromacs website. I'm just wondering what's the meaning of "char *fn" in the xdrfile_???.h as in: /* This function returns the number of atoms in the xtc file in *natoms */ extern int read_xtc_natoms(char *fn,int *natoms

RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs

He Berk, I've sent it to the bugzilla. Could you have a look? Thanks very much! Lanyuan From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs Date: Thu, 29 Jan 2009 23:32:43 +0100 Hi, I just tested it and it runs fine for me

[gmx-users] "nstlist=-1" dosen't work for parallel runs

Hi, Again I have a problem regarding the "nstlist=-1" option and this time it's related to parallel runs. With the help from Berk, I can run my system with nstlist=-1 option and 1 cpu without any problem. However, each time when I run it using more than one cpu under MPI, the run crashes immedi

RE: [gmx-users] "nstlist=-1" and performance problem

+0100 Hi, Any documentation on how this is actually done? Sounds interesting! XAvier. On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:Hi Berk, Thanks very much. I've found the problem. As you said I forgot to increase rvdw. So the buffer is zero and the system needs to update the nblist every step

RE: [gmx-users] "nstlist=-1" and performance problem

Hi, No warning was found. Is it because the use of "User" vdw potential? The mdp file is the following: title= A cpp = cpp include = -I../top define = integrator = md dt = 0.001 nsteps

RE: [gmx-users] "nstlist=-1" and performance problem

Hi Berk, Thanks very much. I've found the problem. As you said I forgot to increase rvdw. So the buffer is zero and the system needs to update the nblist every step, which is obviously wrong. After I corrected the mistake, the speed for "nstlist=-1" is roughly three times faster as I expected.

[gmx-users] "nstlist=-1" and performance problem

Hello, Could Berk or someone else answer my question regarding the new "nstlist=-1" option in gmx4? In my understanding, the algorithm for this option is the one used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with "nstlist=-1" and "nstlist=1", I found the speeds were basical

RE: [gmx-users] a question about template.c

ject: Re: [gmx-users] a question about template.c > > * Nicolas [2008-10-06 17:22:44 -0600]: > >>LuLanyuan a écrit : >>> Hello, >>> When I used template.c to make my own tool, I always got the progress >>> information like >>> "Reading frame

RE: [gmx-users] a question about template.c

- > Date: Mon, 6 Oct 2008 17:22:44 -0600 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a question about template.c > > LuLanyuan a écrit : >> Hello, >> When I used template.c to make my own tool, I always got the progress >>

[gmx-users] a question about template.c

Hello, When I used template.c to make my own tool, I always got the progress information like "Reading frame 60 time 60.000" after the Gromacs copyright information. Sometimes I want to run my tool in background. But these reading frame messages still jump out even after I use the "&"

RE: [gmx-users] cgnr

Hi Lin, Please read the manual. By checking the "Index" section you'll find charge group. For example, there is a paragraph in page 20. Lanyuan Lu > Date: Thu, 21 Aug 2008 09:52:35 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gm

[gmx-users] A bug of trjconv for force output?

Hello All, I just found a strange problem for the gromacs tool trjconv. I have a trajectory (and the tpr file) which contains three groups of molecules and x,v and f. When I use trjconv to output the trajectory of the 1st group, everything is fine. For example, I have A,B and C groups in my tra

RE: [gmx-users] What's the default pbc of Gromacs trajectories?

But usually trr files are huge and the convertion takes time. Thanks, Lanyuan Lu > Date: Mon, 28 Jul 2008 17:07:30 -0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories? > > > > LuLany

[gmx-users] What's the default pbc of Gromacs trajectories?

Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was "whole", which means no broken molecule

RE: [gmx-users] g_wham command issues

I remember that at least for the old version of g_wham, you need to gzip the pdo files first. Lanyuan Lu > Date: Tue, 1 Jul 2008 11:38:18 -0400 > To: gmx-users@gromacs.org > From: [EMAIL PROTECTED] > Subject: [gmx-users] g_wham command issues > > Hello, > > I a

[gmx-users] genbox memory problem

Hello, I have a problem about genbox command in GMX. I'm running genbox to randamly insert molecules. Because the probobility of successful insertion is low, I have to use a large number for the "-try" variable. After running genbox I found sometimes the memory cost increased gradually after ea

RE: [gmx-users] Re: deshuf.ndx doesn't work for forces?

r grompp command. If the output >> of trjconv is gro/pdb, you're right that it's only deshuffled, but not >> de= >> sorted. But since there's no force in the gro >> file, the bug i mentioned is only in the case when you choose trr as >> the = >> output of your deshuffle operation. >&

RE: [gmx-users] deshuf.ndx doesn't work for forces?

00 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] deshuf.ndx doesn't work for forces? > >> Message: 2 >> Date: Wed, 23 Jan 2008 18:56:22 -0500 >> From: LuLanyuan >> Subject: [gmx-users] deshuf.ndx doesn't work for forces?

[gmx-users] deshuf.ndx doesn't work for forces?

Hello All, I found sth like a bug regarding the deshuffle index file. I did a simulation using multiple cpus and -sort -shuffle options. After that I tried to use the deshuf.ndx file to recover the original atom order for my trr file by trjconv -n deshuf.ndx ... command. But by checking the out

RE: [gmx-users] g_wham

Hi, I don't remember whether the bug has been fixed for 3.3.*. Can any gromacs guy clarify that? Abu, have you tried the original g_wham first? If it really dosen't work, please shoot me an email. Then I can send you the correct file. Lanyuan Lu > Date: Fr