Re: [gmx-users] Regarding TCoupling and position restraints

[HANNIBAL LECTER]

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  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  | 
> (410)
> 706-7441
>
> ==**
> --
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[gmx-users] generation of gro file

[Musharaf Ali]

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
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Re: [gmx-users] Regarding TCoupling and position restraints

[Justin Lemkul]

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

==
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Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

[massimo sandal]

On 15 Aug 2013 15:27, "grita"  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
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[gmx-users] Regarding TCoupling and position restraints

[HANNIBAL LECTER]

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?
-- 
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Re: [gmx-users] About Error in mdrun

[Justin Lemkul]

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

==
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Re: [gmx-users] for help about reading xtc file

[Mark Abraham]

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  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  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  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 
> #include 
> #include 
> #include 
>
> 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  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
>>> * Please search the archive at 
>>> http://ww

Re: [gmx-users] Re: Hai friends (balu)

[jkrieger]

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
> --
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>


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[gmx-users] Re: Hai friends (balu)

[Muhammad Naqvi]

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
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Re: [gmx-users] for help about reading xtc file

[Xu, Yechuan]

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  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  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 
 #include 
 #include 
 #include 
 
 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  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
>> * 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!
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> * Can't post? Read http://www.gromacs.org/Support/Mai

Re: [gmx-users] for help about reading xtc file

[Mark Abraham]

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  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  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 
>>> #include 
>>> #include 
>>> #include 
>>>
>>> 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  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

[massimo sandal]

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 

>
> 
> 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
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Re: [gmx-users] for help about reading xtc file

[Xu, Yechuan]

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  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 
>> #include 
>> #include 
>> #include 
>> 
>> 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  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
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[gmx-users] About Error in mdrun

[vidhya sankar]

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
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[gmx-users] Hai friends

[balu]

  
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...



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[gmx-users] Restart REMD

[minwuh081]

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 




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Re: [gmx-users] Restart REMD

[Mark Abraham]

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  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
>
> --
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Re: [gmx-users] LINCS Constraints - all-bonds or h-bonds?

[Erik Marklund]

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  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."  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
>> 
>> -- 
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[gmx-users] Restart REMD

[Min Wu]

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

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Re: [gmx-users] psf to tpr

[Dr. Vitaly Chaban]

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 wrote:

> 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  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
> > --
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Re: [gmx-users] psf to tpr

[Mark Abraham]

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  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
> --
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Re: [gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster

[Mark Abraham]

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  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
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Re: [gmx-users] for help about reading xtc file

[Mark Abraham]

On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan  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 
> #include 
> #include 
> #include 
>
> 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  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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>
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