[gmx-users] psf to tpr
Dear All, I would like to convert my NAMD psf file to GROMACS tpr file? First of all, is it possible? If so, is there any script available? Please help me in this regard. Thanks for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] for help about reading xtc file
On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan y...@neu.edu wrote:
Thank you for your reply. after I read the xdrfile.c,
I changed the sentence as
pos=xdr_getpos((XDR*) (xtc-xdr));
like that in the file of xdrfile.c. I also copy the definition
for XDR and xdr_op to my own code.
You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?
Mark
But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
pos=xdr_getpos((XDR *)(xtc-xdr));
^
here are my code:
#include stdio.h
#include stdlib.h
#include math.h
#include xdrfile_xtc.h
enum xdr_op
{
XDR_ENCODE = 0,
XDR_DECODE = 1,
XDR_FREE = 2
};
typedef struct XDR XDR;
struct XDR
{
enum xdr_op x_op;
struct xdr_ops
{
int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
/* two next routines are not 64-bit IO safe - don't use! */
unsigned int (*x_getpostn) (XDR *__xdrs);
int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
void (*x_destroy) (XDR *__xdrs);
}
*x_ops;
char *x_private;
};
int main(int argc, char *argv[])
{
int i;
int step, read_return, result;
int natoms;
float time,prec=1000.;
matrix box;
rvec *x;
XDRFILE *xtc;
char *fname;
unsigned int pos;
printf(begin, argc=%d\n,argc);
if(argc==2){
fname=argv[1];
}
xtc=xdrfile_open (fname,r);
read_xtc_natoms (fname,natoms);
printf(number of atoms: %d\n,natoms);
x = calloc(natoms, sizeof (x[0]));
while(1){
read_return=read_xtc(xtc,natoms,step,time,box,x,prec);
if (read_return!=0) break;
pos=xdr_getpos((XDR *)(xtc-xdr));
printf(%d\n,pos);
}
xdrfile_close (xtc);
}
Thanks,
YC
On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.
Mark
On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan y...@neu.edu wrote:
Hi Everyone,
I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?
I tried:
XDRFILE *xtc;
unsigned int pos;
pos=xdr_getpos(xtc.xdr);
but I got:
error: request for member ‘xdr’ in something not a structure or union
Thanks in advance.
YC--
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Re: [gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster
It's trying to run a test MPI mdrun (with -version -maxh 0.001) to check that things work, before you get error messages that confuse the issue with doing actual PME run testing. So maybe you need to sort out the run-time working directories to match. See what you need to do to run such an mdrun by hand. You should only get one such error per run of g_tune_pme, not myriads. Mark On Fri, Aug 16, 2013 at 7:38 AM, Jernej Zidar jernej.zi...@gmail.com wrote: Hello, I tried as you suggested but the utility still fails. The job output file contains a myriad of errors like this: Program g_tune_pme, VERSION 4.6.3 Source code file: /home/ihpczidj/scratch/gromacs-4.6.3/src/tools/gmx_tune_pme.c, line: 665 Fatal error: Output from test run could not be found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - - - What kind of output does g_tune_pme try to read if there's no output at that time? Jernej export MPIRUN=$(which srun) should be all you need to help g_tune_pme to understand how to start an MPI calc. g_tune_pme runs in serial, but it needs to *call* srun. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] psf to tpr
I doubt there's a useful script - there's too many details to even have a reliable psf-to-top converter. Google will know if anybody does! Mark On Fri, Aug 16, 2013 at 8:17 AM, Venkat Reddy venkat...@gmail.com wrote: Dear All, I would like to convert my NAMD psf file to GROMACS tpr file? First of all, is it possible? If so, is there any script available? Please help me in this regard. Thanks for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] psf to tpr
No, it is not. But you can at least convert coordinates via VMD. If you want to use gromacs trajectory analysis tools, it is easier to convert NAMD trajectory to gromacs trajectory. Otherwise, I have no idea why one may need to jump between codes. Dr. Vitaly V. Chaban On Fri, Aug 16, 2013 at 10:52 AM, Mark Abraham mark.j.abra...@gmail.comwrote: I doubt there's a useful script - there's too many details to even have a reliable psf-to-top converter. Google will know if anybody does! Mark On Fri, Aug 16, 2013 at 8:17 AM, Venkat Reddy venkat...@gmail.com wrote: Dear All, I would like to convert my NAMD psf file to GROMACS tpr file? First of all, is it possible? If so, is there any script available? Please help me in this regard. Thanks for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Restart REMD
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpirun has exited due to process rank 53 with PID 17572 on node glenn26-3 exiting improperly. There are two reasons this could occur: 1. this process did not call init before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call init. By rule, if one process calls init, then ALL processes must call init prior to termination. 2. this process called init, but exited without calling finalize. By rule, all processes that call init MUST call finalize prior to exiting or it will be considered an abnormal termination This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [glenn25-3.int.private:22036] 17 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [glenn25-3.int.private:22036] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages Is this a bug? how to fix it? Best regards Min -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS Constraints - all-bonds or h-bonds?
I often use 4 fs with all-bonds and virtual sites, especially if lacking sampling is a greater source of error than the kinetic energy being slightly off. Erik On 15 Aug 2013, at 20:58, Michael Shirts mrshi...@gmail.com wrote: I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic energy start being subtly off. H-bonds has less chance of failing with large numbers of constraints- less iteration required, especially if bond system cross parallelization boundaries. If your molecules are 10 atoms, it probably doesn't matter either way. Sent from my iPhone On Aug 15, 2013, at 9:11, Barnett, James W. jbarn...@tulane.edu wrote: Searching through this mailing list it seems like some have stated that with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general. The questions I have are: 1) What are some personal opinions on when it is ok to switch to h-bonds from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general practice? 2) Also, if typically 2 fs and h-bonds are ok, what time-step do users (or you personally) generally go to with all-bonds? I am speaking generally here of course. Thanks for your responses. -- Wes Barnett | jbarn...@tulane.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Restart REMD
Probably the same issue as http://redmine.gromacs.org/issues/1072, which is probably fixed if you update to 4.5.7. Mark On Fri, Aug 16, 2013 at 3:05 PM, Min Wu min...@chem.gu.se wrote: Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpirun has exited due to process rank 53 with PID 17572 on node glenn26-3 exiting improperly. There are two reasons this could occur: 1. this process did not call init before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call init. By rule, if one process calls init, then ALL processes must call init prior to termination. 2. this process called init, but exited without calling finalize. By rule, all processes that call init MUST call finalize prior to exiting or it will be considered an abnormal termination This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [glenn25-3.int.private:22036] 17 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [glenn25-3.int.private:22036] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages Is this a bug? how to fix it? Best regards Min -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Restart REMD
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpirun has exited due to process rank 53 with PID 17572 on node glenn26-3 exiting improperly. There are two reasons this could occur: 1. this process did not call init before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call init. By rule, if one process calls init, then ALL processes must call init prior to termination. 2. this process called init, but exited without calling finalize. By rule, all processes that call init MUST call finalize prior to exiting or it will be considered an abnormal termination This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [glenn25-3.int.private:22036] 17 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [glenn25-3.int.private:22036] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages Is this a bug? how to fix it? Best regards Min -- View this message in context: http://gromacs.5086.x6.nabble.com/Restart-REMD-tp5010542.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Hai friends
http://gromacs.5086.x6.nabble.com/file/n5010545/ss.png Can anyone suggest me to calculate the number of alpha-, 3-10, pi-helical hydrogen bonds in protein using gromacs. Is there any particular commands in gromacs, please let me know... Thank you... -- View this message in context: http://gromacs.5086.x6.nabble.com/Hai-friends-tp5010545.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Error in mdrun
Dear justin Thank you for your previous reply When i run the md in gromacs 4.6.2 with plumed1.3 Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Back Off! I just backed up CNTPEPRSOLIONSfull.trr to ./#CNTPEPRSOLIONSfull.trr.3# Back Off! I just backed up CNTPEPRSOLIONSfull.edr to ./#CNTPEPRSOLIONSfull.edr.3# WARNING: This run will generate roughly 273370 Mb of data starting mdrun 'C225N99O45 in water' 1 steps, 20.0 ps. ! PLUMED ERROR: PluMed dead with errors: check log file ! ABORTING RUN Segmentation fault (core dumped) To avoid this May i use -pin on ? Thnaks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] for help about reading xtc file
Yes, I realized that it is a opaque structure.
I just want to read a certain frame from the
xtc file. For example, last time I read the xtc
file to a certain frame, I want to recorde the
position and next time I can read the xtc file
from there, not from beginning.
Did anybody do that?
Thanks,
YC
On Aug 16, 2013, at 4:39 AM, Mark Abraham wrote:
On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan y...@neu.edu wrote:
Thank you for your reply. after I read the xdrfile.c,
I changed the sentence as
pos=xdr_getpos((XDR*) (xtc-xdr));
like that in the file of xdrfile.c. I also copy the definition
for XDR and xdr_op to my own code.
You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?
Mark
But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
pos=xdr_getpos((XDR *)(xtc-xdr));
^
here are my code:
#include stdio.h
#include stdlib.h
#include math.h
#include xdrfile_xtc.h
enum xdr_op
{
XDR_ENCODE = 0,
XDR_DECODE = 1,
XDR_FREE = 2
};
typedef struct XDR XDR;
struct XDR
{
enum xdr_op x_op;
struct xdr_ops
{
int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
/* two next routines are not 64-bit IO safe - don't use! */
unsigned int (*x_getpostn) (XDR *__xdrs);
int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
void (*x_destroy) (XDR *__xdrs);
}
*x_ops;
char *x_private;
};
int main(int argc, char *argv[])
{
int i;
int step, read_return, result;
int natoms;
float time,prec=1000.;
matrix box;
rvec *x;
XDRFILE *xtc;
char *fname;
unsigned int pos;
printf(begin, argc=%d\n,argc);
if(argc==2){
fname=argv[1];
}
xtc=xdrfile_open (fname,r);
read_xtc_natoms (fname,natoms);
printf(number of atoms: %d\n,natoms);
x = calloc(natoms, sizeof (x[0]));
while(1){
read_return=read_xtc(xtc,natoms,step,time,box,x,prec);
if (read_return!=0) break;
pos=xdr_getpos((XDR *)(xtc-xdr));
printf(%d\n,pos);
}
xdrfile_close (xtc);
}
Thanks,
YC
On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.
Mark
On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan y...@neu.edu wrote:
Hi Everyone,
I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?
I tried:
XDRFILE *xtc;
unsigned int pos;
pos=xdr_getpos(xtc.xdr);
but I got:
error: request for member ‘xdr’ in something not a structure or union
Thanks in advance.
YC--
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Re: [gmx-users] Hai friends
If you want the residues in a particular secondary structure, you can use do_dssp, see http://manual.gromacs.org/current/online/do_dssp.html . g_hbonds can calculate hydrogen bonds. To separate the h-bonds by secondary structure, I suppose some scripting is needed. 2013/8/16 balu balu2...@vit.ac.in http://gromacs.5086.x6.nabble.com/file/n5010545/ss.png Can anyone suggest me to calculate the number of alpha-, 3-10, pi-helical hydrogen bonds in protein using gromacs. Is there any particular commands in gromacs, please let me know... Thank you... -- View this message in context: http://gromacs.5086.x6.nabble.com/Hai-friends-tp5010545.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] for help about reading xtc file
That's only worth bothering with if you'll do that re-read several
times. Is writing out the frame(s) of interest a better solution?
Mark
On Fri, Aug 16, 2013 at 6:25 PM, Xu, Yechuan y...@neu.edu wrote:
Yes, I realized that it is a opaque structure.
I just want to read a certain frame from the
xtc file. For example, last time I read the xtc
file to a certain frame, I want to recorde the
position and next time I can read the xtc file
from there, not from beginning.
Did anybody do that?
Thanks,
YC
On Aug 16, 2013, at 4:39 AM, Mark Abraham wrote:
On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan y...@neu.edu wrote:
Thank you for your reply. after I read the xdrfile.c,
I changed the sentence as
pos=xdr_getpos((XDR*) (xtc-xdr));
like that in the file of xdrfile.c. I also copy the definition
for XDR and xdr_op to my own code.
You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?
Mark
But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
pos=xdr_getpos((XDR *)(xtc-xdr));
^
here are my code:
#include stdio.h
#include stdlib.h
#include math.h
#include xdrfile_xtc.h
enum xdr_op
{
XDR_ENCODE = 0,
XDR_DECODE = 1,
XDR_FREE = 2
};
typedef struct XDR XDR;
struct XDR
{
enum xdr_op x_op;
struct xdr_ops
{
int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
/* two next routines are not 64-bit IO safe - don't use! */
unsigned int (*x_getpostn) (XDR *__xdrs);
int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
void (*x_destroy) (XDR *__xdrs);
}
*x_ops;
char *x_private;
};
int main(int argc, char *argv[])
{
int i;
int step, read_return, result;
int natoms;
float time,prec=1000.;
matrix box;
rvec *x;
XDRFILE *xtc;
char *fname;
unsigned int pos;
printf(begin, argc=%d\n,argc);
if(argc==2){
fname=argv[1];
}
xtc=xdrfile_open (fname,r);
read_xtc_natoms (fname,natoms);
printf(number of atoms: %d\n,natoms);
x = calloc(natoms, sizeof (x[0]));
while(1){
read_return=read_xtc(xtc,natoms,step,time,box,x,prec);
if (read_return!=0) break;
pos=xdr_getpos((XDR *)(xtc-xdr));
printf(%d\n,pos);
}
xdrfile_close (xtc);
}
Thanks,
YC
On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.
Mark
On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan y...@neu.edu wrote:
Hi Everyone,
I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?
I tried:
XDRFILE *xtc;
unsigned int pos;
pos=xdr_getpos(xtc.xdr);
but I got:
error: request for member ‘xdr’ in something not a structure or union
Thanks in advance.
YC--
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Re: [gmx-users] for help about reading xtc file
If the xdrfile library can't do what I want, writing out
the frames is an alternative. I know that the MDAnalysis
has modified the xdrfile library to do seeking xtc file.
But it seems that they do a python wrapper.
Thanks,
YC
On Aug 16, 2013, at 12:35 PM, Mark Abraham wrote:
That's only worth bothering with if you'll do that re-read several
times. Is writing out the frame(s) of interest a better solution?
Mark
On Fri, Aug 16, 2013 at 6:25 PM, Xu, Yechuan y...@neu.edu wrote:
Yes, I realized that it is a opaque structure.
I just want to read a certain frame from the
xtc file. For example, last time I read the xtc
file to a certain frame, I want to recorde the
position and next time I can read the xtc file
from there, not from beginning.
Did anybody do that?
Thanks,
YC
On Aug 16, 2013, at 4:39 AM, Mark Abraham wrote:
On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan y...@neu.edu wrote:
Thank you for your reply. after I read the xdrfile.c,
I changed the sentence as
pos=xdr_getpos((XDR*) (xtc-xdr));
like that in the file of xdrfile.c. I also copy the definition
for XDR and xdr_op to my own code.
You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?
Mark
But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
pos=xdr_getpos((XDR *)(xtc-xdr));
^
here are my code:
#include stdio.h
#include stdlib.h
#include math.h
#include xdrfile_xtc.h
enum xdr_op
{
XDR_ENCODE = 0,
XDR_DECODE = 1,
XDR_FREE = 2
};
typedef struct XDR XDR;
struct XDR
{
enum xdr_op x_op;
struct xdr_ops
{
int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
/* two next routines are not 64-bit IO safe - don't use! */
unsigned int (*x_getpostn) (XDR *__xdrs);
int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
void (*x_destroy) (XDR *__xdrs);
}
*x_ops;
char *x_private;
};
int main(int argc, char *argv[])
{
int i;
int step, read_return, result;
int natoms;
float time,prec=1000.;
matrix box;
rvec *x;
XDRFILE *xtc;
char *fname;
unsigned int pos;
printf(begin, argc=%d\n,argc);
if(argc==2){
fname=argv[1];
}
xtc=xdrfile_open (fname,r);
read_xtc_natoms (fname,natoms);
printf(number of atoms: %d\n,natoms);
x = calloc(natoms, sizeof (x[0]));
while(1){
read_return=read_xtc(xtc,natoms,step,time,box,x,prec);
if (read_return!=0) break;
pos=xdr_getpos((XDR *)(xtc-xdr));
printf(%d\n,pos);
}
xdrfile_close (xtc);
}
Thanks,
YC
On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.
Mark
On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan y...@neu.edu wrote:
Hi Everyone,
I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?
I tried:
XDRFILE *xtc;
unsigned int pos;
pos=xdr_getpos(xtc.xdr);
but I got:
error: request for member ‘xdr’ in something not a structure or union
Thanks in advance.
YC--
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[gmx-users] Re: Hai friends (balu)
If the goal is to simply count the secondary structure, pass the dssp output file through grep __ dssp_output.xpm | wc Fill in the dssp code for each secondary structure in the underline separately. Grep would extract all characters that fit that pattern and wc would count it. Hope that helps. Ali -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Hai friends (balu)
I suppose there would also be a way of passing do_dssp output on to make_ndx then you could use the index with g_hbond to count hbonds in each secondary structure element. Best wishes James If the goal is to simply count the secondary structure, pass the dssp output file through grep __ dssp_output.xpm | wc Fill in the dssp code for each secondary structure in the underline separately. Grep would extract all characters that fit that pattern and wc would count it. Hope that helps. Ali -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] for help about reading xtc file
It can be done either way. Whether to do it is up to you. The compiler
is obviously reporting that your attempt to duplicate the code wasn't
far-reaching enough. I suggest that extending the interface in the
header file to return the position, and also to seek to a given
position is a much better approach than duplication. Now your new code
can work where the opaque structs are not intended to be opaque... If
it works well, you can contribute it back for others. But a crude hack
will stay un-reused :-)
Mark
On Fri, Aug 16, 2013 at 7:02 PM, Xu, Yechuan y...@neu.edu wrote:
If the xdrfile library can't do what I want, writing out
the frames is an alternative. I know that the MDAnalysis
has modified the xdrfile library to do seeking xtc file.
But it seems that they do a python wrapper.
Thanks,
YC
On Aug 16, 2013, at 12:35 PM, Mark Abraham wrote:
That's only worth bothering with if you'll do that re-read several
times. Is writing out the frame(s) of interest a better solution?
Mark
On Fri, Aug 16, 2013 at 6:25 PM, Xu, Yechuan y...@neu.edu wrote:
Yes, I realized that it is a opaque structure.
I just want to read a certain frame from the
xtc file. For example, last time I read the xtc
file to a certain frame, I want to recorde the
position and next time I can read the xtc file
from there, not from beginning.
Did anybody do that?
Thanks,
YC
On Aug 16, 2013, at 4:39 AM, Mark Abraham wrote:
On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan y...@neu.edu wrote:
Thank you for your reply. after I read the xdrfile.c,
I changed the sentence as
pos=xdr_getpos((XDR*) (xtc-xdr));
like that in the file of xdrfile.c. I also copy the definition
for XDR and xdr_op to my own code.
You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?
Mark
But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
pos=xdr_getpos((XDR *)(xtc-xdr));
^
here are my code:
#include stdio.h
#include stdlib.h
#include math.h
#include xdrfile_xtc.h
enum xdr_op
{
XDR_ENCODE = 0,
XDR_DECODE = 1,
XDR_FREE = 2
};
typedef struct XDR XDR;
struct XDR
{
enum xdr_op x_op;
struct xdr_ops
{
int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
/* two next routines are not 64-bit IO safe - don't use! */
unsigned int (*x_getpostn) (XDR *__xdrs);
int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
void (*x_destroy) (XDR *__xdrs);
}
*x_ops;
char *x_private;
};
int main(int argc, char *argv[])
{
int i;
int step, read_return, result;
int natoms;
float time,prec=1000.;
matrix box;
rvec *x;
XDRFILE *xtc;
char *fname;
unsigned int pos;
printf(begin, argc=%d\n,argc);
if(argc==2){
fname=argv[1];
}
xtc=xdrfile_open (fname,r);
read_xtc_natoms (fname,natoms);
printf(number of atoms: %d\n,natoms);
x = calloc(natoms, sizeof (x[0]));
while(1){
read_return=read_xtc(xtc,natoms,step,time,box,x,prec);
if (read_return!=0) break;
pos=xdr_getpos((XDR *)(xtc-xdr));
printf(%d\n,pos);
}
xdrfile_close (xtc);
}
Thanks,
YC
On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.
Mark
On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan y...@neu.edu wrote:
Hi Everyone,
I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?
I tried:
XDRFILE *xtc;
unsigned int pos;
pos=xdr_getpos(xtc.xdr);
but I got:
error: request for member ‘xdr’ in something not a structure or union
Thanks in advance.
YC--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] About Error in mdrun
On 8/16/13 11:51 AM, vidhya sankar wrote: Dear justin Thank you for your previous reply When i run the md in gromacs 4.6.2 with plumed1.3 Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Back Off! I just backed up CNTPEPRSOLIONSfull.trr to ./#CNTPEPRSOLIONSfull.trr.3# Back Off! I just backed up CNTPEPRSOLIONSfull.edr to ./#CNTPEPRSOLIONSfull.edr.3# WARNING: This run will generate roughly 273370 Mb of data starting mdrun 'C225N99O45 in water' 1 steps, 20.0 ps. ! PLUMED ERROR: PluMed dead with errors: check log file ! ABORTING RUN Segmentation fault (core dumped) To avoid this May i use -pin on ? It's easier to try it and see (and have an answer in seconds) rather than wait several hours to get a reply... The specific answer depends on your hardware and whether or not you are going to see any benefit. I don't really know the mechanics of this process, though there have been numerous discussions in recent weeks and months. First, upgrade to 4.6.3, then try again. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding TCoupling and position restraints
Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
On 15 Aug 2013 15:27, grita cemilyi...@arcor.de wrote In short, the sigma is the separation or the 'diameter'. True or False ??? Neither. The diameter of a particle is a meaningless concept here. You have a continuous potential, not a definite boundary. If you want your particles to *almost* never come closer than a certain distance, you need the potential to be positive and much higher than the average thermal energy at that distance. How to translate this in numbers depends on your specific needs. -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010526.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding TCoupling and position restraints
On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] generation of gro file
Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. Here the xyz coordinates are attached for 18-crown-6. Thank in advance. Regards New learner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding TCoupling and position restraints
Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
