RE: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Hi, I quickly ran the tpr file you provided on bugzilla, but I don't see an enormous energy drift. What do you mean with "the energy explodes"? Berk Date: Wed, 21 Apr 2010 11:18:53 -0400 Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.

Re: [gmx-users] The problems of controling one atom through modifygromacs sourse code

Hi Chuan, you might want to take a look at gmx_ga2la.h. The function ga2la_home provides the local atom number for a given global atom number (or returns FALSE if the atom is not found on the local processor). Carsten On Apr 21, 2010, at 4:40 PM, 聂雪川 wrote: > Hi,gmx-users, >Now I want to c

[gmx-users] Understanding template.c

Hi gmx users !! I want to read the trajectory file (*.trr ), produced as a result of mdrun. I came to know that a file template.c already exists to facilate my process. I could compile and execute the template.c. Like printf("Atom name: %s\n",*(top.atoms.atomname[n])); printf("Atom charge: %f\n",t

Re: [gmx-users] Understanding template.c

On 22/04/2010 7:11 PM, Chandan Choudhury wrote: Hi gmx users !! I want to read the trajectory file (*.trr ), produced as a result of mdrun. I came to know that a file template.c already exists to facilate my process. I could compile and execute the template.c. Like printf("Atom name: %s\n",*(top

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, I have run it for 5ns, as you said for first 1ns i have not seen much drift in the energy there after energy is slowly increasing in each step. Should i run it again and send you the edr file? can you please let me know on which version of gromacs you have run this file? Thanks very m

[gmx-users] the error for 2D periodic boundary

 Hello,  when I use the 2D periodic boundary for the pr run , it just ran several steps then exited,  the log file has some error message like this : Program mdrun, VERSION 4.0.5 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each part

[gmx-users] .mtx file

Hello, I am trying to calculate the normal mode analysis for ionic liquids. I could do energy minimzation. I could not get .mtx file for further analysis to get normal modes. THis is my energy minimization file define = -DFLEXIBLE constraints = none integrator

Re: [gmx-users] .mtx file

Nilesh Dhumal wrote: Hello, I am trying to calculate the normal mode analysis for ionic liquids. I could do energy minimzation. I could not get .mtx file for further analysis to get normal modes. THis is my energy minimization file define = -DFLEXIBLE constraints

[gmx-users] make_edi

Hi When I run make_edi with a small eigenvec.trr file it works, but gives me a segmentation fault when I input large .trr files generated using g_covar. These large eigenvector files work well with g_anaeig and I have used them to generate projections as well as filtered trajectories. The comm

[gmx-users] Magic error xtc?

Hello, I am running simulations and I got Magic Number error: Fatal error: Magic Number Error in XTC file (read 0, should be 1995) Checking file md.part0002.xtc Reading frame 0 time 48190.004 # Atoms 6533 Precision 0.001 (nm) Reading frame 178000 time 83790.008 Part one of the simu

Re: [gmx-users] Magic error xtc?

nishap.pa...@utoronto.ca wrote: Hello, I am running simulations and I got Magic Number error: Fatal error: Magic Number Error in XTC file (read 0, should be 1995) Checking file md.part0002.xtc Reading frame 0 time 48190.004 # Atoms 6533 Precision 0.001 (nm) Reading frame 178000 t

Re: [gmx-users] Magic error xtc?

Hi Justin, Well the way I continued my second part of the simulation was using my md.cpt file. I checked my .cpt file and this is what I got: Last frame -1 time 83786.961 , so I guess my second run updated the file, so does this mean I have to do the whole simulation again? or c

Re: [gmx-users] Magic error xtc?

nishap.pa...@utoronto.ca wrote: Hi Justin, Well the way I continued my second part of the simulation was using my md.cpt file. I checked my .cpt file and this is what I got: Last frame -1 time 83786.961 , so I guess my second run updated the file, so does this mean I have to do t

RE: [gmx-users] make_edi, more info

Hi I have included the output from two make_edi submissions, the first one gave a segmentation fault and the second did not. The only difference between the two is the input .trr file. :-) make_edi (-: Option Filename Type Description -

[gmx-users] No Temperature Coupling to protein

Hi gmx users, I'd like to run a test simulation, in which the temperature coupling is not on for the protein, yet active for the solvent and ions. If I specify in the tc-grps only "Non-protein", the grompp complains (Fatal error) that there are some atoms (the ones of the protein) out

Re: [gmx-users] Magic error xtc?

Hey, Otherwise it's also still possible to do old style continuation with a frame from the .trr/.edr file, provided you have those... Cheers, Tsjerk On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul wrote: > > > nishap.pa...@utoronto.ca wrote: >> >> Hi Justin, >> >>    Well the way I continued

Re: [gmx-users] No Temperature Coupling to protein

Ricardo O. S. Soares wrote: Hi gmx users, I'd like to run a test simulation, in which the temperature coupling is not on for the protein, yet active for the solvent and ions. If I specify in the tc-grps only "Non-protein", the grompp complains (Fatal error) that there are some atom

Re: [gmx-users] Magic error xtc?

I am trying using prev_md.cpt file. I checked and it looks okay, so hopefully it will work. If not I will try using .trr files. Thanks Quoting Tsjerk Wassenaar : Hey, Otherwise it's also still possible to do old style continuation with a frame from the .trr/.edr file, provided you have tho

Re: [gmx-users] .mtx file

Hello Justin, I could genrate the .mtx file. I followed following steps. g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr g_nmtraj -s 1.tpr -v test1.trr -o test.xtc g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg and g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -

Re: [gmx-users] .mtx file

Nilesh Dhumal wrote: Hello Justin, I could genrate the .mtx file. I followed following steps. g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr g_nmtraj -s 1.tpr -v test1.trr -o test.xtc g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg and g_nmens -v test1.trr -e e

Re: [gmx-users] .mtx file

Hello Justin In manual (Manual-4.0) and g_nmens -h (help), the extension of output file is .xtc. If I use the default output file name still I am getting the same error. Nilesh On Thu, April 22, 2010 4:01 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> I could genr

Re: [gmx-users] .mtx file

Nilesh Dhumal wrote: Hello Justin In manual (Manual-4.0) and g_nmens -h (help), the extension of output file is .xtc. If I use the default output file name still I am getting the same error. I know what the help information says, I was just trying to clarify if what you had shown was actu

[gmx-users] Re: No Temperature Coupling to protein (Justin A. Lemkul)

Oh yes I see, thanks Justin! Ricardo O. S. Soares wrote: > Hi gmx users, > > I'd like to run a test simulation, in which the temperature coupling > is not on for the protein, yet active for the solvent and ions. If I > specify in the tc-grps only "Non-protein", the

[gmx-users] grompp, energy minimization,, output file error

Dear gmx users, I am trying to run grompp program to preprocess the input files. input gro file contains coordinates of a stack of hexane molecules (256 molecules). grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em -maxwarn 30 >& output.grompp_em my problem is that output: Hex

Re: [gmx-users] grompp, energy minimization,, output file error

On 23/04/2010 8:52 AM, Moeed wrote: Dear gmx users, I am trying to run grompp program to preprocess the input files. input gro file contains coordinates of a stack of hexane molecules (256 molecules). grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em -maxwarn 30 >& output.grom

Re: [gmx-users] grompp, energy minimization,, output file error

Moeed wrote: Dear gmx users, I am trying to run grompp program to preprocess the input files. input gro file contains coordinates of a stack of hexane molecules (256 molecules). grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em -maxwarn 30 >& output.grompp_em my probl

RE: [gmx-users] grompp, energy minimization,, output file error

For starters there is no residue name in your .gro file, you simply have a number.  First column should be … 1HEX  C1 1HEX C2 . . . 1HEX H14 2HEX C1 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parad

[gmx-users] more than one peptide in one simulation box

Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf , I tried to

Re: [gmx-users] more than one peptide in one simulation box

On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insert