[gmx-users] regarding error in editconf

Dear friends when I am trying command editconf, it is showing error File input/output error I have protein of 700 amino acids and its of inverted T shape and we are giving boxtype dodecahedron. input command is: editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0 with regard

[gmx-users] regarding installation

Dear friends, i have installed gromacs 4.5-beta3 and fftw-3.2.8 on root, now when I am giving command ./configure --enable-threads, it is showing error: cannot find fftw3f library. please let me know, why this error is showing here? thank you in advance Anamika -- gmx-users m

[gmx-users] trying to install gromacs on linux single processor

hello all, I am trying to install new version of gromacs on linux single processor, getting this error ./configure --enable-threads --enable-float checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install..

[gmx-users] need help

Dear gromacs user, I want to install gromacs new version on my linux system. can u all please guide me, Thanking u in advance Anamika -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] RMSD graph

Dear All, Please tell, what should I predict from this graph? I can understand this is normal type of graph. Sorry for inconvenience, but I want to ask some questions, my this job crashed many time, because of power shut down and I had to restart this again and again, I used tp

[gmx-users] regarding rmsd !!

Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD and RMSF for this 16 ns simulation, without stopping the running simulation.it was crashed before, so I used tpbconv -f previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2 t

[gmx-users] regarding trjconv

Dear all, RMSD and RMSF of my protein is showing abnormal flucutuation. To overcome this problem I am using following commands--> trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump

[gmx-users] fatal error in minimization

Dear Friends, I extracted few conformation from my running job by using trjconv. but now as I want to minimize this conformation it is showing Fatal error that *.pdb and *.top coordinates does not match. I gave this command for my minimization grompp -f em.mdp -c *.pdb -o em.tpr

[gmx-users] extract conformations !!

Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000

[gmx-users] Re:confusion regarding tpbconv

> Thanks in advance. > > > On Mon, 12 May 2008 15:10:32 +0530 > "Anamika Awasthi" <[EMAIL PROTECTED]> wrote: >> Dear Friends, >>If my simulation crashed because of power failure, then as I know >> there are two option to restart the Job. >>

[gmx-users] confusion regarding tpbconv

Dear Xavier Thanks for your help, after running my tpbconv I got this Reading toplogy and shit from 2ao2_tpxout.tpr Reading file 2ao2_tpxout.tpr, VERSION 3.3 (single precision) READING COORDS, VELS AND BOX FROM TRAJECTORY 2ao2_tpxout.trr... trn version: GMX_trn_file (single precision) Read fra

[gmx-users] confusion regarding tpbconv

Dear Friends, If my simulation crashed because of power failure, then as I know there are two option to restart the Job. One is GROMPP and another is 'tpbconv', in 'grompp' we have to do some changes in md.mdp, but 'tpbconv' takes everything automatically, tpbconv needs only .trr a

[gmx-users] about fourier grid

Dear Gromacs user, Please tell me what is the significance of fourier grid and spacing in MD simulation? Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] log file has converted into.log.swp file

Dear Gromacs Users, Please help me to recover my important log file from swap file, How can I do this? I am wondering wheather I can get my original file or not. E325: ATTENTION Found a swap file by the name ".md2.log.swp" owned by: anamika dated: Wed Apr 16 04:21:09 2008 fil

[gmx-users] how can I restart simulation

Dear Gromacs Users, I have done MD simulation for 15 ns and I need simulation for further 5 ns. I am wondering how is this possible? Thank you in advance Anamika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

[gmx-users] wants to simulate for more timesteps

Dear Gromacs Users, I have simulated my protein for 15 ns, I need to simulate it for more. How can I do this? Is this any easy way that it can restart after previous 15 ns? Thanks in advance -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA

[gmx-users] abnormal RMSD

e first 330 atoms of the run input file. You can make a matching run input file with tpbconv." with regards Anamika -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road,

[gmx-users] Abnormal RMSD

Dear all, Thanks Florian and Justin for your suggestions I am an beginner, so I am writing all the commands which I used pdb2gmx -f *.pdb -o *.gro -p *.top then editconf -f *.gro -o *out.gro -c -d 0.8 genbox -cp *out.gro -cs -o *b4ion.gro -p *.top grompp -f em.mdp -po *out.mdp -c *b4i

[gmx-users] abnormal RMSD

Thankyou Justin for your suggestion I tried this command---> trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole this was showing this error "can not open file topol.tpr" then I repeated the same command with "-s topol.tpr" then trjconv -f trajout_whole.trr -o trajout_

[gmx-users] Abnormal fluctuation in RMSD

Dear all, I am working on a biological dimer of 330 residues. I dont think that I got any error message when I did grompp. Please find pr.mdp filesbelow and RMSD as attachment. Please tell me why it happened? pr.mdp ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file t

[gmx-users] subscription

-- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] Hello

fluctuation its till 2.5 nm. Please Tell me how should I analyze this and How can I sort out this problem. Thanking you -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA