-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 10/13/2010 02:08 PM, Florian Dommert wrote: > On 10/13/2010 01:01 PM, Eudes Fileti wrote: >> Hi Florian, thank you for your help! >> I informed at the file.mdp that the velocities should be saved: > >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 10 >> nstvout = 10 >> nstfout = 0 >> ; > > > Hi, > > I took a quick look at the code and realized that the problem is the -m > flag. I will try to fix this and report ASAP. > > > /Flo > >
Hello,
there is a wrong check in line 164/165:
if (bMol)
bTPS = bM || ftp2bSet(efTPS,NFILE,fnm) ||
!ftp2bSet(efNDX,NFILE,fnm);
It should be:
if (bMol || bM)
bTPS = ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
If you change this lines in src/tools/gmx_velacc.c and recompile,
everything should work fine.
Attached there is a patch against the master branch which should fix the
issue.
/Flo
P.S Perhaps a developer can commit this patch :)
>
>
>> Also, I checked the trajectory using gmxcheck and I got this:
>
>> Checking file traj.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame 0 time 0.000
>> # Atoms 7178
>> Last frame 150000 time 3000.000
>
>
>> Item #frames Timestep (ps)
>> Step 150001 0.02
>> Time 150001 0.02
>> Lambda 150001 0.02
>> Coords 150001 0.02
>> Velocities 150001 0.02
>> Forces 0
>> Box 150001 0.02
>
>
>> So I believe that velocities are OK.
>> I've been using version 4.5 and not version 4.5.1,
>> Do you believe that's the problem? Or it could be memory problem?
>> _______________________________________
>> Eudes Eterno Fileti
>> Centro de Ciências Naturais e Humanas
>> Universidade Federal do ABC CCNH
>> Av. dos Estados, 5001
>> Santo André - SP - Brasil
>> CEP 09210-971
>> http://fileti.ufabc.edu.br
>
>
>
>> On 10/12/2010 11:12 PM, Eudes Fileti wrote:
>> > Hi everybody, I'm trying to use g_velacc to calculate the diffusion
>> > coeficient for my solute.
>> > For this, I performed a simple simulation to test such tool.
>> >
>> > 1000 water molecules,
>> > NPT ensemble
>> > positions and velocities colected every 0.01ps
>> > Gromacs 4.5.
>> >
>> > However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen
>> > 1000 -nonormalize
>> >
>> > I get the following error:
>> >
>> > Group 0 ( System) has 3000 elements
>> > Group 1 ( SOL) has 3000 elements
>> > Group 2 ( OW) has 1000 elements
>> > Group 3 ( HW1) has 1000 elements
>> > Group 4 ( HW2) has 1000 elements
>> > Select a group: 1
>> > Selected 1: 'SOL'
>> > trn version: GMX_trn_file (single precision)
>> > Reading frame 0 time 0.000 Segmentation fault
>
>> Recently I used g_velacc in gmx 4.0.7 and it worked fine. Now I just
>> tested the gmx4.5.1 version for you and it also worked. So it seems that
>> there is something wrong with your trajectory. Are you sure that
>> velocities were saved, which is not the case for an xtc file. You have
>> to explicitly define nstvout in your mdp file, that tells gromacs how
>> often the velocities should be written to the trr file.
>
>> /Flo
>
>> >
>> > I've tried several things. I changed flag values. I tried the -mol
>> > option. I tried converting a trajectory
>> > to another format (.trj). I tried using the version 3.3.3 of g_velacc.
>> > Nothing worked, always the same error.
>> > Could someone give me a hand?
>> > Grateful
>> > eef
>> > _______________________________________
>> > Eudes Eterno Fileti
>> > Centro de Ciências Naturais e Humanas
>> > Universidade Federal do ABC CCNH
>> > Av. dos Estados, 5001
>> > Santo André - SP - Brasil
>> > CEP 09210-971
>> > http://fileti.ufabc.edu.br
>> >
>
>
>> - --
>> Florian Dommert
>> Dipl.-Phys.
>
>> Institute for Computational Physics
>
>> University Stuttgart
>
>> Pfaffenwaldring 27
>> 70569 Stuttgart
>
>> Phone: +49(0)711/685-6-3613
>> Fax: +49-(0)711/685-6-3658
>
>> EMail: [email protected]
>> <mailto:[email protected]>
>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
>
>
>
>
- --
Florian Dommert
Dipl.-Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Phone: +49(0)711/685-6-3613
Fax: +49-(0)711/685-6-3658
EMail: [email protected]
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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diff --git a/src/tools/gmx_velacc.c b/src/tools/gmx_velacc.c
index d656889..b2bbd9a 100644
--- a/src/tools/gmx_velacc.c
+++ b/src/tools/gmx_velacc.c
@@ -162,8 +162,8 @@ int gmx_velacc(int argc,char *argv[])
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
- if (bMol)
- bTPS = bM || ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
+ if (bMol || bM)
+ bTPS = ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
if (bTPS) {
bTop=read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,
g_velacc.patch.sig
Description: Binary data
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