Well I'm keeping struggling with this script. Apparently the problem in in using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp file with integrator steep works. while with md it always gives the error message that it cannot open the .xtc file.<br>
How can I get around this problem?<br>I can only see two ways now: <br>-either there is a way to use md with GROMACS 3.3.1<br>-or there is a way so that the mdrun of a newer version of GROMACS can deal with the file. If I try, even specifying the path for each .itp file, then the program cannot find certain atomtypes, such as<br>
Atomtype CH2R not found<br>any suggestions here?<br>Thanks<br>Francesca<br><br><br><br><div class="gmail_quote">2012/1/31 Francesca Vitalini <span dir="ltr"><<a href="mailto:francesca.vitalini11@gmail.com">francesca.vitalini11@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thank you Justin for your quick reply. Unfortunately I cannot use a more modern version of GROMACS as my topology and .gro files where first created for a reverse transformation from cg to fg and thus required the 3.3.1 version and some specific .itp files that are only present in that version. If I try to run it all with GORMACS 4.5 that it crashes immediately.<br>
I've also tried without the -cpo option but it doesn't change anything.<br>
I've checked the permission on the folder and as I supposed I have total access to it so it might not effect the results.<br>
If I open with vi a file with the same name as the .xtc file that I need for the script and write in it some crap just to try and then I just re run the mrdun command I don't get the error message anymore but gromacs complains saying<br>
<div class="im">Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision)<br>
Loaded with Money<br>
<br>
</div>WARNING: Incomplete frame: nr 0 time 0<br>
Segmentation fault<br>
I have checked with gmxcheck the .trr input file as it was suggested in another discussion, and apparently it is ok, so I really don't know what to do.<br>
Can you help me with that?<br>
Thanks<br>
Francesca<br>
<br>
<br>
Il giorno 31/gen/2012, alle ore 14.33, Justin A. Lemkul ha scritto:<br>
<div class="HOEnZb"><div class="h5"><br>
><br>
><br>
> Francesca Vitalini wrote:<br>
>> Actually the directory is of my own and I have created it in my home directory so that shouldn't be a problem as I also have created other files in the same directory without any problems so far.<br>
>> Other ideas? Thanks<br>
>> Francesca<br>
>> Il giorno 31/gen/2012, alle ore 13.02, Justin A. Lemkul ha scritto:<br>
>>><br>
>>> francesca vitalini wrote:<br>
>>>> Hallo GROMACS users!<br>
>>>> I'm trying to run a simple md script after running an energy minimization script on my system and I'm getting a wired error message<br>
>>>> Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision)<br>
>>>> Loaded with Money<br>
>>>> -------------------------------------------------------<br>
>>>> Program mdrun, VERSION 3.3.1<br>
>>>> Source code file: gmxfio.c, line: 706<br>
>>>> Can not open file:<br>
>>>> coarse.xtc<br>
>>>> it is strange as the coarse.xtc file should be created by running the mdrun command.<br>
>>> Sounds to me like you don't have permission to write in the working directory.<br>
>>><br>
>>> -Justin<br>
>>><br>
>>>> that is my submition command line<br>
>>>> $MYGROMACSPATH/bin/mdrun -v -s dynamin_dimer_PR1.tpr -o dynamin_dimer_PR1.trr -cpo dynamin_dimer_PR1.cpt -c dynamin_dimer_PR1.gro<br>
>>>> the .tpr file had been previously created by grompp<br>
><br>
> I don't know if this is a problem or not, but I just noticed it. If you're using version 3.3.1, the -cpo option doesn't exist. mdrun won't exit with a fatal error in this case, but you still shouldn't be using it.<br>
><br>
> Aside from that, I would suggest you use a more modern version of Gromacs (4.5.5) rather than one that is certifiably ancient. There may well have been some bug that was fixed 6 years ago that no one even remembers ;)<br>
><br>
>>>> $MYGROMACSPATH/bin/grompp -v -f pr1.mdp -c dynamin_dimer_EM_solvated.gro -p dynamin_dimer_fg.top -o dynamin_dimer_PR1.tpr<br>
>>>> and the .mdp file I'm using is<br>
><br>
> The .mdp file contains a number of redundancies, which should have caused grompp to fail. Also probably irrelevant, but worth noting.<br>
><br>
> -Justin<br>
><br>
>>>> cpp = /lib/cpp<br>
>>>> constraints = all-bonds<br>
>>>> integrator = md<br>
>>>> tinit = 0.0<br>
>>>> dt = 0.002<br>
>>>> nsteps = 40000<br>
>>>> nstcomm = 0<br>
>>>> nstxout = 10000<br>
>>>> nstvout = 10000<br>
>>>> nstfout = 10000<br>
>>>> nstlog = 10000<br>
>>>> nstenergy = 100<br>
>>>> nstxtcout = 100<br>
>>>> xtc_precision = 1000<br>
>>>> nstlist = 10<br>
>>>> energygrps = Protein<br>
>>>> ns_type = grid<br>
>>>> rlist = 0.9<br>
>>>> coulombtype = Generalized-Reaction-Field<br>
>>>> epsilon_rf = 62<br>
>>>> rcoulomb = 1.5<br>
>>>> rvdw = 1.0<br>
>>>> ;Tcoupl = nose-hoover<br>
>>>> ;tc-grps = Protein<br>
>>>> ;ref_t = 300<br>
>>>> nstxtcout = 100<br>
>>>> xtc_precision = 1000<br>
>>>> nstlist = 10<br>
>>>> energygrps = Protein<br>
>>>> ns_type = grid<br>
>>>> rlist = 0.9<br>
>>>> coulombtype = Generalized-Reaction-Field<br>
>>>> epsilon_rf = 62<br>
>>>> rcoulomb = 1.5<br>
>>>> rvdw = 1.0<br>
>>>> ;Tcoupl = nose-hoover<br>
>>>> ;tc-grps = Protein<br>
>>>> ;ref_t = 300<br>
>>>> ;tau_t = 0.1<br>
>>>> ; Temperature coupling<br>
>>>> tcoupl = Berendsen ; Couple temperature to external heat bath according to Berendsen method<br>
>>>> tc-grps = Protein Non-Protein ; Use separate heat baths for Protein and Non-Protein groups<br>
>>>> tau_t = 0.1 0.1 ; Coupling time constant, controlling strength of coupling<br>
>>>> ref_t = 200 200 ; Temperature of heat bat<br>
>>>> I have also tried to change the .mdp file but I get the same error message.<br>
>>>> If I try to use a mdrun from a different version of GROMACS it complains again as it is not the same as grompp.<br>
>>>> Do you have any tips for solving this problem?<br>
>>>> Thanks<br>
>>>> Francesca<br>
>>> --<br>
>>> ========================================<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>>><br>
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> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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</div></div></blockquote></div><br>