from:"Amit Choubey"

[gmx-users] Re: Using CHARMM 36 for DPPC simulation

2011-11-11 Thread Amit Choubey

Hi Everyone,

I did another simulation where i found the the DPPC area per lipid is 0.61
nm^2 . Is this acceptable ?

I have seen issues like this on the mailing list before can one of the
experts give me some hints.

Amit

On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey kgp.a...@gmail.com wrote:


 5Hello all,

 I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
 following so far:

 1. Download pdb file containing 128 DPPC molecules from
 http://www.charmm-gui.org/?doc=archivelib=lipid_pure

 2. I separated one lipid molecule from the obtained pdb file and used
 pdb2gmx -f 1dppc.gro -nochargegrp

 The top file obtained was converted to itp file by commenting few things
 out.

 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer
 from CHARMM GUI for the box length. I used editconf to convert the pdb to
 gro and manually inserted the box size in the gro file.

 4. Created a system.top file which looks like
 #include charmm36.ff/forcefield.itp
 #include lipid.itp
 #include charmm36.ff/tips3p.itp

 [ system ]
 chol

 [ molecules ]
 DPPC 128
 SOL  3659

 5. I used following mdp settings

 integrator = md ; leap-frog integrator
 nsteps = 2000 ; 40 ns
 dt = 0.002 ; 2 fs

 ; Output control
 nstxout = 10 ; save coordinates every 200 ps
 nstvout = 10 ; save velocities every 200 ps
 nstenergy = 1 ; save energies every 2 ps
 nstlog = 1 ; update log file every 2 ps

 ; Neighborsearching
 ns_type = grid ; search neighboring grid cels
 nstlist = 10 ; 10 fs
 rlist = 1.0 ; short-range neighborlist cutoff (in nm)
 rlistlong = 1.4
 vdwtype = switch
 rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
 rvdw_switch = 0.8

 ; Electrostatics
 rcoulomb= 1.0
 rcoulomb_switch = 0.0
 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
 pme_order = 6 ; cubic interpolation
 fourierspacing = 0.15 ; grid spacing for FFT

 ; Temperature coupling is on
 tcoupl = Nose-Hoover ; More accurate thermostat
 tc-grps = DPPC SOL  ; two coupling groups - more accurate
 tau_t = 0.2 0.2 ; time constant, in ps
 ref_t = 323.15 323.15 ; reference temperature, one for each group, in K

 ; Pressure coupling is on
 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
 pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
 independent z
 tau_p = 5.0 ; time constant, in ps
 ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
 compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1

 ; Periodic boundary conditions
 pbc = xyz ; 3-D PBC

 ; Dispersion correction
 DispCorr = No ; account for cut-off vdW scheme


 ; Velocity generation
 gen_vel =  yes
 gen_temp=  200.0
 gen_seed=  173529

 ; COM motion removal
 nstcomm = 1
 comm-mode   = Linear
 comm-grps   = DPPC SOL

 ; Energy monitoring
 energygrps  =  DPPC SOL

 ; Bond parameters
 constraint_algorithm = lincs; holonomic constraints
 constraints = hbonds ; all bonds (even heavy atom-H bonds)
 constrained
 lincs_iter  = 1 ; accuracy of LINCS
 lincs_order = 4 ; also related to accuracy

 The resulting simulation gave me an area per lipid =0.591 nm^2. This is
 not quite right. Can somebody suggest what else could i do it get close to
 the 0.63 nm^2 value.

 Also when i looked at trajectory file it seemed that the box length was
 not set up quite right because the downloaded pdb file looked ok with the
 membrane in the middle but at the next frame the membrane was at a totally
 different location. The leaflets were separated and the middle of the
 membrane was at the edge of the box.

 Also when i used pdb2gmx -nochargegrp on the downloaded file it created a
 gro file whose system size was
8.20170   8.64120   6.54740 in contrast to6.4   6.4
 6.38452 .

 Amit

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[gmx-users] Using CHARMM 36 for DPPC simulation

2011-11-09 Thread Amit Choubey

5Hello all,

I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
following so far:

1. Download pdb file containing 128 DPPC molecules from
http://www.charmm-gui.org/?doc=archivelib=lipid_pure

2. I separated one lipid molecule from the obtained pdb file and used
pdb2gmx -f 1dppc.gro -nochargegrp

The top file obtained was converted to itp file by commenting few things
out.

3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer
from CHARMM GUI for the box length. I used editconf to convert the pdb to
gro and manually inserted the box size in the gro file.

4. Created a system.top file which looks like
#include charmm36.ff/forcefield.itp
#include lipid.itp
#include charmm36.ff/tips3p.itp

[ system ]
chol

[ molecules ]
DPPC 128
SOL  3659

5. I used following mdp settings

integrator = md ; leap-frog integrator
nsteps = 2000 ; 40 ns
dt = 0.002 ; 2 fs

; Output control
nstxout = 10 ; save coordinates every 200 ps
nstvout = 10 ; save velocities every 200 ps
nstenergy = 1 ; save energies every 2 ps
nstlog = 1 ; update log file every 2 ps

; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rlistlong = 1.4
vdwtype = switch
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
rvdw_switch = 0.8

; Electrostatics
rcoulomb= 1.0
rcoulomb_switch = 0.0
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 6 ; cubic interpolation
fourierspacing = 0.15 ; grid spacing for FFT

; Temperature coupling is on
tcoupl = Nose-Hoover ; More accurate thermostat
tc-grps = DPPC SOL  ; two coupling groups - more accurate
tau_t = 0.2 0.2 ; time constant, in ps
ref_t = 323.15 323.15 ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1

; Periodic boundary conditions
pbc = xyz ; 3-D PBC

; Dispersion correction
DispCorr = No ; account for cut-off vdW scheme


; Velocity generation
gen_vel =  yes
gen_temp=  200.0
gen_seed=  173529

; COM motion removal
nstcomm = 1
comm-mode   = Linear
comm-grps   = DPPC SOL

; Energy monitoring
energygrps  =  DPPC SOL

; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints = hbonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

The resulting simulation gave me an area per lipid =0.591 nm^2. This is not
quite right. Can somebody suggest what else could i do it get close to the
0.63 nm^2 value.

Also when i looked at trajectory file it seemed that the box length was not
set up quite right because the downloaded pdb file looked ok with the
membrane in the middle but at the next frame the membrane was at a totally
different location. The leaflets were separated and the middle of the
membrane was at the edge of the box.

Also when i used pdb2gmx -nochargegrp on the downloaded file it created a
gro file whose system size was
   8.20170   8.64120   6.54740 in contrast to6.4   6.4
6.38452 .

Amit
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Re: [gmx-users] distance between mass center of two groups

2011-08-28 Thread Amit Choubey

Use g_dist tool.

On Sun, Aug 28, 2011 at 8:38 AM, Sajad Ahrari sajadahr...@yahoo.com wrote:

 Dear users,
 is there any command in Gromacs to show fluctuations of distance, between
 mass center for two groups of amino-acids in  a protein, over time?
 thanks,
 sajad

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Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

2011-08-19 Thread Amit Choubey

On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian xiansh...@gmail.com wrote:

 I have sent this email days ago, but I got no answer.

 Hope someone would saw it this time. 

 Sorry for disturbing.

 Dear all:

  I am using gromacs-4.0.2_localpressure to calculate the local
 pressure of my system.

  I have a question.

  When rerun the mdrun from gromacs-4.0.2_localpressure I used a new
 .mdp file. There are some changes of the new .mdp file according the
 original one. I have 2 questions:

 **1.  **I changed the The coulomb interaction type from PME to
 reaction field with epsilon_r=1 epsilon_rf=78;  Is this change feasible?

Yes, you have to switch to cutoff for coulomb interaction. I have seen in
other publications that they use a regular coulomb  with cutoff as large as
2 nm. I am not sure whether there is any advantage in using Reaction field.

 

 **2.  **I used LINCS for all bonds in the simulation, and I still use
 the LINCS for all bonds when calculate the local pressure. Is this way
 right?

 I have had no problems in using LINCS during local pressure calculation.

 

 ** **

 Thanks for any reply.

 ** **

 Best wishes, 

 KONG Xian

 Tsinghua, Beijing, China



 


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Re: [gmx-users] use of the mailing list

2011-08-19 Thread Amit Choubey

On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker junior.nebe...@gmail.comwrote:

 Sure Mark.  If your interest is in patrolling the Gromacs mailing list,
 then I'll leave you to it.


I think before you type your response you should consider that Mark has
helped several hundred times over this mailing list.


 On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 19/08/2011 1:41 PM, Junior Nebeker wrote:

 Correct.  Other people (who are new to this list) need your help, and
 unless their requests are way out of line, there's no reason to adopt a
 haughty attitude in responding.


 There's never a case for rudeness, but when (for example) people have been
 asking questions on the mailing list for years and still haven't absorbed
 the advice available here http://www.gromacs.org/Support, then one can
 get frustrated. Expressing a little of that can help people realise how to
 participate more effectively in the discussion. One's family doctor can ask
 a lot of patient questions about what is wrong because you're paying them a
 lot of money. If people who might give free help don't feel that their time
 is valued, they might stop giving it. One way of demonstrating this is to
 ask questions that show one's willingness to work on the problem by
 providing lots of relevant diagnostic information. See
 http://www.catb.org/~esr/faqs/smart-questions.html

 Mark

 P.S. I'm not intending to express particular criticism of the original
 poster in this thread


 On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 19/08/2011 9:32 AM, Junior Nebeker wrote:


 Hey mark,

 If you are really sick of asking people for such information, why do you
 even care to respond to this mailing list?


  Because I'd rather teach someone to fish than either give them fish or
 watch them starve.


 Mark
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Re: [gmx-users] how to simulate a line charge

2011-08-14 Thread Amit Choubey

Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and no
pbc. Am i missing something ?

On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.com wrote:

 I was not sure if changing the size of maxcg would not negatively influence
 anything else. I will give it a try. Thanks Justin


 On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 I change the maximum charge group size defined in the
 include/types/nblist.h header from 32 to 267. Then grompp worked fine but
 the mdrun did not start. The following error came out

 Program mdrun_jptlc, VERSION 4.5.3
 Source code file: ns.c, line: 2417

 Fatal error:
 Max #atoms in a charge group: 267  64


  /* Verify whether largest charge group is = max cg.*
  * This is determined by the type of the local exclusion type *
  * Exclusions are stored in bits. (If the type is not large*
  * enough, enlarge it, unsigned char - unsigned short - unsigned
 long)*
  */


 The solution is described in the comment above.


  maxcg = sizeof(t_excl)*8;


 Increase the size here.

 -Justin


  if (nr_in_cg  maxcg)
 {
 gmx_fatal(FARGS,Max #atoms in a charge group: %d  %d\n,
   nr_in_cg,maxcg);
 }


 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] how to simulate a line charge

2011-08-14 Thread Amit Choubey

Following is the mdp file

cpp =  /usr/bin/cpp
;define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
nsteps  =  1
;
;   Energy minimizing stuff
;
emtol   =  200
emstep  =  0.01
pbc = no
nstcomm =  0
ns_type =  grid
coulombtype = Cut-off
rlist   =  60
rcoulomb=  60
rvdw=  60
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no

E_x = 1 0 0
E_y = 1 0 0
E_z = 1 0 0


Following is the energy term

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
1.11496e-070.0e+000.0e+009.90561e+059.90561e+05
 Pressure (bar)
0.0e+00

   Step   Time Lambda
  11.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
7.55922e-020.0e+000.0e+009.90324e+059.90324e+05
 Pressure (bar)
0.0e+00


Amit

On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Justin, when i define the whole line charge as a charge group i do get a
 coulomb energy contribution. I thought there would be no non-bonded
 contribution. I use a very high cut-off (longer than chain length) and no
 pbc. Am i missing something ?


 Without seeing your .mdp file and the actual energy terms you're observing,
 I can only guess.  One would think that if it is the only molecule in the
 system, there should be no intermolecular Coulombic terms (unless maybe some
 arise due to periodicity, but in that case you do not have an infinite
 system and then they are artifacts).  There may be intramolecular terms
 (like 1-4) or PME-related terms.

 -Justin

  On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.commailto:
 kgp.a...@gmail.com wrote:

I was not sure if changing the size of maxcg would not negatively
influence anything else. I will give it a try. Thanks Justin


On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:



Amit Choubey wrote:

I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp
worked fine but the mdrun did not start. The following error
came out

Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417

Fatal error:
Max #atoms in a charge group: 267  64


/* Verify whether largest charge group is = max cg.*
 * This is determined by the type of the local exclusion
type *
 * Exclusions are stored in bits. (If the type is not
 large*
 * enough, enlarge it, unsigned char - unsigned short
- unsigned long)*
 */


The solution is described in the comment above.


maxcg = sizeof(t_excl)*8;


Increase the size here.

-Justin


if (nr_in_cg  maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d 
%d\n,
  nr_in_cg,maxcg);
}


-- ==**__==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080


 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin

 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

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Re: [gmx-users] how to simulate a line charge

2011-08-14 Thread Amit Choubey

sorry i did not mention it but the E field contribution should be zero, i am
sure about it. Also when i make all the cutoff = 0 the energy terms are
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
1.11496e-070.0e+000.0e+001.03128e+061.03128e+06
 Pressure (bar)
0.0e+00

   Step   Time Lambda
  11.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
7.49142e-020.0e+000.0e+001.03104e+061.03104e+06
 Pressure (bar)
0.0e+00

Coulomb (SR) is quite close but not exactly equal to previous case when
cutoff is 60 nm.

On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Following is the mdp file

 cpp =  /usr/bin/cpp
 ;define  =  -DFLEX_SPC
 constraints =  none
 integrator  =  steep
 nsteps  =  1
 ;
 ;   Energy minimizing stuff
 ;
 emtol   =  200
 emstep  =  0.01
 pbc = no
 nstcomm =  0
 ns_type =  grid
 coulombtype = Cut-off rlist   =  60
 rcoulomb=  60
 rvdw=  60
 Tcoupl  =  no
 Pcoupl  =  no
 gen_vel =  no

 E_x = 1 0 0
 E_y = 1 0 0
 E_z = 1 0 0


 Following is the energy term

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
1.11496e-070.0e+000.0e+009.90561e+059.90561e+05
  Pressure (bar)
0.0e+00

   Step   Time Lambda
  11.00.0

   Energies (kJ/mol)
   Bond  AngleLJ (SR)   Coulomb (SR)  Potential
7.55922e-020.0e+000.0e+009.90324e+059.90324e+05
  Pressure (bar)
0.0e+00



 I suspect that energy terms comes from the use of an electric field, which
 you had not mentioned before.

 -Justin

  Amit


 On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:

Justin, when i define the whole line charge as a charge group i
do get a coulomb energy contribution. I thought there would be
no non-bonded contribution. I use a very high cut-off (longer
than chain length) and no pbc. Am i missing something ?


Without seeing your .mdp file and the actual energy terms you're
observing, I can only guess.  One would think that if it is the only
molecule in the system, there should be no intermolecular Coulombic
terms (unless maybe some arise due to periodicity, but in that case
you do not have an infinite system and then they are artifacts).
 There may be intramolecular terms (like 1-4) or PME-related terms.

-Justin

On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey
kgp.a...@gmail.com mailto:kgp.a...@gmail.com
mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote:

   I was not sure if changing the size of maxcg would not
 negatively
   influence anything else. I will give it a try. Thanks Justin


   On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
   mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Amit Choubey wrote:

   I change the maximum charge group size defined in the
   include/types/nblist.h header from 32 to 267. Then
 grompp
   worked fine but the mdrun did not start. The
following error
   came out

   Program mdrun_jptlc, VERSION 4.5.3
   Source code file: ns.c, line: 2417

   Fatal error:
   Max #atoms in a charge group: 267  64


   /* Verify whether largest charge group is = max
 cg.*
* This is determined by the type of the local
exclusion
   type *
* Exclusions are stored in bits. (If the type is
not large*
* enough, enlarge it, unsigned char - unsigned
short
   - unsigned long)*
*/


   The solution is described in the comment above.


   maxcg = sizeof(t_excl)*8;


   Increase the size here.

   -Justin


   if (nr_in_cg  maxcg)
   {
   gmx_fatal(FARGS,Max #atoms in a charge
group: %d 
   %d\n,
 nr_in_cg,maxcg

Re: [gmx-users] how to simulate a line charge

2011-08-13 Thread Amit Choubey

I change the maximum charge group size defined in the include/types/nblist.h
header from 32 to 267. Then grompp worked fine but the mdrun did not start.
The following error came out

Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417

Fatal error:
Max #atoms in a charge group: 267  64

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

In ns.c the relevant section (in bold) is the following:


void init_ns(FILE *fplog,const t_commrec *cr,
 gmx_ns_t *ns,t_forcerec *fr,
 const gmx_mtop_t *mtop,
 matrix box)
{
int  mt,icg,nr_in_cg,maxcg,i,j,jcg,ngid,ncg;
t_block *cgs;
char *ptr;

/* Compute largest charge groups size (# atoms) */
nr_in_cg=1;
for(mt=0; mtmtop-nmoltype; mt++) {
cgs = mtop-moltype[mt].cgs;
for (icg=0; (icg  cgs-nr); icg++)
{
nr_in_cg=max(nr_in_cg,(int)(cgs-index[icg+1]-cgs-index[icg]));
}
}

   * /* Verify whether largest charge group is = max cg.*
* * This is determined by the type of the local exclusion type *
* * Exclusions are stored in bits. (If the type is not large*
* * enough, enlarge it, unsigned char - unsigned short - unsigned
long)*
* */*
*maxcg = sizeof(t_excl)*8;*
*if (nr_in_cg  maxcg)*
*{*
*gmx_fatal(FARGS,Max #atoms in a charge group: %d  %d\n,*
*  nr_in_cg,maxcg);*
*}*

ngid = mtop-groups.grps[egcENER].nr;
snew(ns-bExcludeAlleg,ngid);
for(i=0; ingid; i++) {
ns-bExcludeAlleg[i] = TRUE;
for(j=0; jngid; j++)
{
if (!(fr-egp_flags[i*ngid+j]  EGP_EXCL))
{
ns-bExcludeAlleg[i] = FALSE;
}
}
}

if (fr-bGrid) {
/* Grid search */
ns-grid = init_grid(fplog,fr);
init_nsgrid_lists(fr,ngid,ns);
}
else
{
/* Simple search */
snew(ns-ns_buf,ngid);
for(i=0; (ingid); i++)
{
snew(ns-ns_buf[i],SHIFTS);
}
ncg = ncg_mtop(mtop);
snew(ns-simple_aaj,2*ncg);
for(jcg=0; (jcgncg); jcg++)
{
ns-simple_aaj[jcg] = jcg;
ns-simple_aaj[jcg+ncg] = jcg;
}
}

/* Create array that determines whether or not atoms have VdW */
snew(ns-bHaveVdW,fr-ntype);
for(i=0; (ifr-ntype); i++)
{
for(j=0; (jfr-ntype); j++)
{
ns-bHaveVdW[i] = (ns-bHaveVdW[i] ||
   (fr-bBHAM ?
((BHAMA(fr-nbfp,fr-ntype,i,j) != 0) ||
 (BHAMB(fr-nbfp,fr-ntype,i,j) != 0) ||
 (BHAMC(fr-nbfp,fr-ntype,i,j) != 0)) :
((C6(fr-nbfp,fr-ntype,i,j) != 0) ||
 (C12(fr-nbfp,fr-ntype,i,j) != 0;
}
}
if (debug)
pr_bvec(debug,0,bHaveVdW,ns-bHaveVdW,fr-ntype,TRUE);

ns-nra_alloc = 0;
ns-bexcl = NULL;
if (!DOMAINDECOMP(cr))
{
/* This could be reduced with particle decomposition */
ns_realloc_natoms(ns,mtop-natoms);
}

ns-nblist_initialized=FALSE;

/* nbr list debug dump */
{
char *ptr=getenv(GMX_DUMP_NL);
if (ptr)
{
ns-dump_nl=strtol(ptr,NULL,10);
if (fplog)
{
fprintf(fplog, GMX_DUMP_NL = %d, ns-dump_nl);
}
}
else
{
ns-dump_nl=0;
}
}
}


Any ideas ?
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Re: [gmx-users] how to simulate a line charge

2011-08-13 Thread Amit Choubey

Thanks Bogdan, defining each atom as a charge group solves the grompp issue.
Also here the atoms interact via non-bonded potentials. I think its a better
way to simulate the line charge.

Amit

On Sat, Aug 13, 2011 at 8:29 AM, Bogdan Costescu bcoste...@gmail.comwrote:

 On Sat, Aug 13, 2011 at 05:43, Amit Choubey kgp.a...@gmail.com wrote:
  The largest charge group contains 267 atoms. The maximum is 32.

 Column 6 in the [atoms] section of the .top file defines the charge
 group. If you want each atom to be in its own charge group, you can
 set this to the same number as the atom number (column 1).

 Cheers,
 Bogdan
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Re: [gmx-users] how to simulate a line charge

2011-08-13 Thread Amit Choubey

I was not sure if changing the size of maxcg would not negatively influence
anything else. I will give it a try. Thanks Justin

On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 I change the maximum charge group size defined in the
 include/types/nblist.h header from 32 to 267. Then grompp worked fine but
 the mdrun did not start. The following error came out

 Program mdrun_jptlc, VERSION 4.5.3
 Source code file: ns.c, line: 2417

 Fatal error:
 Max #atoms in a charge group: 267  64


  /* Verify whether largest charge group is = max cg.*
  * This is determined by the type of the local exclusion type *
  * Exclusions are stored in bits. (If the type is not large*
  * enough, enlarge it, unsigned char - unsigned short - unsigned
 long)*
  */


 The solution is described in the comment above.


  maxcg = sizeof(t_excl)*8;


 Increase the size here.

 -Justin


  if (nr_in_cg  maxcg)
 {
 gmx_fatal(FARGS,Max #atoms in a charge group: %d  %d\n,
   nr_in_cg,maxcg);
 }


 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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[gmx-users] how to simulate a line charge

2011-08-12 Thread Amit Choubey

Hi all,

I am trying to do a calculation on an artificial line charge in vacuum. The
line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term. I defined the required itp files
and top file. When i issue

grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp

I get the following error message.

Program grompp_jpt, VERSION 4.5.3
Source code file: grompp.c, line: 175

Fatal error:
The largest charge group contains 267 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What should i try to do to circumvent this error.

Thanks
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Re: [gmx-users] how to simulate a line charge

2011-08-12 Thread Amit Choubey

On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Amit Choubey wrote:

Hi all,

I am trying to do a calculation on an artificial line charge in vacuum.
The line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term. I defined the required itp

If you're trying to keep the atoms in a line, the system will not be
stable. Angles of 180 degrees routinely crash.

Not even if i use a 3 body angle term with equilibrium angle = 180? If not
then why ?

files and top file. When i issue

grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp

I get the following error message.

Program grompp_jpt, VERSION 4.5.3
Source code file: grompp.c, line: 175

Fatal error:
The largest charge group contains 267 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the
GROMACS
website at
http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors

What should i try to do to circumvent this error.

The maximum charge group size is defined in the include/types/nblist.h
header. You can alter the value there, which will get around the error, but
consider whether or not this is even a good physical model. If all atoms
are in the same charge group, there are no electrostatic interactions
between these atoms since neighbor searching is done and short-range
energies are calculated based on inter-charge group distances. I have no
idea how to properly simulate a line of positively-charged particles, but be
aware.

Thanks for the pointer and the awareness remark. But since this is a model
system and for the physical problem i am trying to deal with its alright if
the atoms within the line charge do not interact via non-bonded potentials.

-Justin

--
==**==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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Re: [gmx-users] Dimensionless units question

2011-07-29 Thread Amit Choubey

Hi,

reduced units works for LJ particles only. I am not sure if it works when
you include electrostatics. When you set charge = 1 it is 1electronic
charge. I would suggest not to use the reduced units for LJ in this
scenario.

Amit

On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote:

 Hi all,

 I'm trying to calculate the force on one particle and the total
 electrostatic energy of my system, which consists of a lattice of 25 evenly
 spaced charges in the xy plane and a single charge in the center above to
 preserve charge neutrality. The reference values I have been given are in
 dimensionless units, so I am tasked with either converting my output to
 dimensionless units or having gromacs work in reduced units from the get go.
 I have set the mass of each charge to 1, the magnitude of the charge on each
 particle to 1, and the values of the C6 and C12 parameters in my itp file to
 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation.
 I've turned off temperature coupling because this is purely a test of the
 handling of electrostatics with 3D Ewald summation plus the correction for
 slab geometry. However, the force and energy I calculate are still quite far
 from the reference values. Have I missed anything if I want my output to be
 in dimensionless units?

 Thanks,
 Alex

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Re: [gmx-users] Dimensionless units question

2011-07-29 Thread Amit Choubey

I am not sure what you want to measure. You mentioned that force and energy
I calculate are still quite far from the reference values, now are you only
looking at electrostatic contributions to these or the total contributions?
If its total contribution then LJ parameters should also be correct and for
that you should switch to standard gromacs units.

Also why do you need to use gmx.ff, seems to me that you already have the
parameters (ie the LJ parameters and charges)

On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall amars...@uwo.ca wrote:

 Hi Amit,

 So if I understand you correctly, any LJ interaction I impose on these
 particles will be quite arbitrary because I'm only concerned with
 electrostatics, right? How then might I go about comparing the dimensionless
 reference values given with the values I calculated? I don't think I can
 simply compare their ratios, as there would still be a unit of length to
 deal with.

 Thanks,
 Alex

 On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi,

 reduced units works for LJ particles only. I am not sure if it works when
 you include electrostatics. When you set charge = 1 it is 1electronic
 charge. I would suggest not to use the reduced units for LJ in this
 scenario.

 Amit

 On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote:

 Hi all,

 I'm trying to calculate the force on one particle and the total
 electrostatic energy of my system, which consists of a lattice of 25 evenly
 spaced charges in the xy plane and a single charge in the center above to
 preserve charge neutrality. The reference values I have been given are in
 dimensionless units, so I am tasked with either converting my output to
 dimensionless units or having gromacs work in reduced units from the get go.
 I have set the mass of each charge to 1, the magnitude of the charge on each
 particle to 1, and the values of the C6 and C12 parameters in my itp file to
 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation.
 I've turned off temperature coupling because this is purely a test of the
 handling of electrostatics with 3D Ewald summation plus the correction for
 slab geometry. However, the force and energy I calculate are still quite far
 from the reference values. Have I missed anything if I want my output to be
 in dimensionless units?

 Thanks,
 Alex

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Re: [gmx-users] Dimensionless units question

2011-07-29 Thread Amit Choubey

On Fri, Jul 29, 2011 at 12:14 PM, Alex Marshall amars...@uwo.ca wrote:

 I'm trying to calculate the total electrostatic energy of the system, and
 the force in the Z direction on the particle placed above the lattice. It's
 a purely electrostatic problem, ideally LJ shouldn't come into it at all,

but I don't know how else to convert the resulting energy and force to
 dimensionless units, which I must do because I was given reference values in
 dimensionless units.


Why not use 0 for LJ parameters? You will have to figure out the units of
energy and force in the reference otherwise you cannot make the comparison.




 I guess I'm not actually using gmx.ff, I was just using the C6-C12
 convention for LJ parameters used in that forcefield's ffnonbonded.itp.

 On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey kgp.a...@gmail.com wrote:

 I am not sure what you want to measure. You mentioned that force and
 energy I calculate are still quite far from the reference values, now are
 you only looking at electrostatic contributions to these or the total
 contributions? If its total contribution then LJ parameters should also be
 correct and for that you should switch to standard gromacs units.

 Also why do you need to use gmx.ff, seems to me that you already have the
 parameters (ie the LJ parameters and charges)


 On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall amars...@uwo.ca wrote:

 Hi Amit,

 So if I understand you correctly, any LJ interaction I impose on these
 particles will be quite arbitrary because I'm only concerned with
 electrostatics, right? How then might I go about comparing the dimensionless
 reference values given with the values I calculated? I don't think I can
 simply compare their ratios, as there would still be a unit of length to
 deal with.

 Thanks,
 Alex

 On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.comwrote:

 Hi,

 reduced units works for LJ particles only. I am not sure if it works
 when you include electrostatics. When you set charge = 1 it is 1electronic
 charge. I would suggest not to use the reduced units for LJ in this
 scenario.

 Amit

 On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote:

 Hi all,

 I'm trying to calculate the force on one particle and the total
 electrostatic energy of my system, which consists of a lattice of 25 
 evenly
 spaced charges in the xy plane and a single charge in the center above to
 preserve charge neutrality. The reference values I have been given are in
 dimensionless units, so I am tasked with either converting my output to
 dimensionless units or having gromacs work in reduced units from the get 
 go.
 I have set the mass of each charge to 1, the magnitude of the charge on 
 each
 particle to 1, and the values of the C6 and C12 parameters in my itp file 
 to
 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation.
 I've turned off temperature coupling because this is purely a test of the
 handling of electrostatics with 3D Ewald summation plus the correction for
 slab geometry. However, the force and energy I calculate are still quite 
 far
 from the reference values. Have I missed anything if I want my output to 
 be
 in dimensionless units?

 Thanks,
 Alex

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Re: [gmx-users] Re: local pressure v4.5 issues

2011-07-28 Thread Amit Choubey

I just checked that the mdrun of v4.0.2_local_pressure can read the tpr
generated from grompp of v4.0.7. I did get some local pressure numbers. Also
i checked the potential energy between 4.0.2 and 4.0.7 there is a difference
of about 0.0008% .

I am just wondering how this problem got fixed ie how could 4.0.2 did not
have trouble reading the tpr of 4.0.7 whereas 4.0.2 could not make the tpr
file (it complains about Invalid dihedral type 9).

On Thu, Jul 28, 2011 at 12:05 AM, Jianguo Li ljg...@yahoo.com.sg wrote:

Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give
this tpr file to v4.0.2_local_pressure to rerun the simulation.

Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
*Cc:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Thursday, 28 July 2011 09:27:04

*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

Hi all,

I am trying to figure out a way to port tpr files (which has CHARMM FF)
from v4.5 to v4.0.2. This is because i want to use the localpressure
calculation which works only in version 4.0.2.

When i issue the following command i get

grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp

I get the following error
*
*

Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure

Source code file: topdirs.c, line: 118

Fatal error:

Invalid dihedral type 9

I think dihedral type 9 is not defined until version 4.0.7. Could anyone
provide a way to deal with this ?

Amit

On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

I downloaded v4.5 and v4.0 from the same websites as you mentioned in
previous email. I am not sure why v4.5 give inconsistent results. I haven't
try v4.0, because my simulation is using CHARMM FF. Could you give more
details of conversion tpr files from v4.5 to v4.0 using CHARMM FF?

Thank you very much!

Cheers,
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
*Cc:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Friday, 1 July 2011 11:47:58

*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

I also encountered the same problem you mentioned.
In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one
file localpressure.dat0. I tested first several frames of a trajectory,
the calculated pressure is not the average of the pressure of individual
frames.

In v4.5 it outputs the profile for frames in separate files which is ok.
My concern is what exactly is going in v 4.0 where there is only one file
for all the frames.

Also where did you download v4.5 and v4.0 from ?

Btw, did you use CHARMM FF in your simulations and how did you convert the
tpr files from v 4.5 to v 4.0?

Yes i have used CHARMM FF and i will have to figure out the conversion.

Cheers
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS
users gmx-users@gromacs.org
*Sent:* Friday, 1 July 2011 10:32:07
*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

Hello Everyone,

The git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used
gromacs-4.0.2_localpressure.tar.gzftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file localpressure.dat .
On the contrary in v 4.5 there were separate localpressure.dat* files for
each frame.

I am not sure what exactly is the content of localpressure.dat. Does it
have the time averaged value of pressure tensor for each voxel ? It doesnt
seem so to me because i tried it over only two frames (3 reruns were done
for two frames separately and a .trr which had these two frames only) and
the numbers did not seem to be averages.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.comwrote:

On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sgwrote:

Hi Amit,

May I ask you a question?
In your calculation of local pressure using a trajectory file, did you
get a single averaged localpressure.dat file? Or else you get a bunch of
separate files for each frame (e.g., localpressure.dat0,
localpressure.dat1,
localpressure.dat2 )?

Yes I do get different files for different trajectories. All the files
seem to have the same problem ie a very large/small number printed

[gmx-users] minor trjconv issue

2011-07-28 Thread Amit Choubey

Hi all,

When i use the following

trjconv_without_shock -f all_molecules_500ns_fixedpbc.gro -o traj.gro -novel
-s npt.tpr

traj.gro still has velocities.


Amit
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Re: [gmx-users] minor trjconv issue

2011-07-28 Thread Amit Choubey

done

On Thu, Jul 28, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi all,

 When i use the following

 trjconv_without_shock -f all_molecules_500ns_fixedpbc.**gro -o traj.gro
 -novel -s npt.tpr

 traj.gro still has velocities.


 Please file an issue report on redmine.gromacs.org so it can be fixed.  I
 know I've seen this reported before, but if there's no official record then
 it likely will never get fixed.

 -Justin

 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Re: local pressure v4.5 issues

2011-07-27 Thread Amit Choubey

Hi all,

I am trying to figure out a way to port tpr files (which has CHARMM FF) from
v4.5 to v4.0.2. This is because i want to use the localpressure calculation
which works only in version 4.0.2.

When i issue the following command i get

grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp

I get the following error
*
*

Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure

Source code file: topdirs.c, line: 118

Fatal error:

Invalid dihedral type 9

I think dihedral type 9 is not defined until version 4.0.7. Could anyone
provide a way to deal with this ?

Amit

On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

Thank you very much!

Cheers,
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
*Cc:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Friday, 1 July 2011 11:47:58

*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

In v4.5 it outputs the profile for frames in separate files which is ok. My
concern is what exactly is going in v 4.0 where there is only one file for
all the frames.

Also where did you download v4.5 and v4.0 from ?

Btw, did you use CHARMM FF in your simulations and how did you convert the
tpr files from v 4.5 to v 4.0?

Yes i have used CHARMM FF and i will have to figure out the conversion.

Cheers
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users
gmx-users@gromacs.org
*Sent:* Friday, 1 July 2011 10:32:07
*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

Hello Everyone,

The git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used
gromacs-4.0.2_localpressure.tar.gzftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file localpressure.dat . On
the contrary in v 4.5 there were separate localpressure.dat* files for
each frame.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote:

On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

Yes I do get different files for different trajectories. All the files
seem to have the same problem ie a very large/small number printed as tensor
elements of the pressure for some of the voxels.

Do you have such problems ? Could we compare our methodologies to use the
local pressure version ?

Amit

Thank you very much!

Cheers,
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Monday, 20 June 2011 07:08:03
*Subject:* [gmx-users] Re: local pressure v4.5 issues

Dear all,

I did another simulation with only SPC water. Then I used the local
pressure gromacs to calculate the stresses. It seems to be reasonable.

I am not sure how to figure out what goes wrong with my previous
simulations when plugged into the local pressure gromacs.

Could someone help me in figuring out whats the issue ?

Thank You.

On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.comwrote:

Dear all,

I installed the git version of local pressure calculation from

http

[gmx-users] gromacs 4.0 vs 4.5

2011-07-19 Thread Amit Choubey

Hi all,

I am doing dppc-water simulation. I am using structure and topologies from

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

In version 4.0 when i do
grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top

it creates npt.tpr without any errors.

Using the same structure and topologies when i issue

grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top

it gives out the following warning

Largest charge group radii for Van der Waals: 5.354, 5.297 nm
Largest charge group radii for Coulomb:   5.354, 5.297 nm
WARNING 1 [file npt.mdp]:
  The sum of the two largest charge group radii (10.650990) is larger than
  rlist (1.20)

I dont think the charge group should be so big. Can someone suggest what is
going on ?

Ami
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Re: [gmx-users] gromacs 4.0 vs 4.5

2011-07-19 Thread Amit Choubey

Thanks Justin, I can see that there is no problem when i fix the
periodicity.

Amit

On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Amit Choubey wrote:

Hi all,

I am doing dppc-water simulation. I am using structure and topologies from

http://moose.bio.ucalgary.ca/**index.php?page=Structures_and_**Topologieshttp://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

In version 4.0 when i do grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp
-p system.top

it creates npt.tpr without any errors.

Using the same structure and topologies when i issue

grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top

it gives out the following warning

Largest charge group radii for Van der Waals: 5.354, 5.297 nm
Largest charge group radii for Coulomb: 5.354, 5.297 nm
WARNING 1 [file npt.mdp]:
The sum of the two largest charge group radii (10.650990) is larger than
rlist (1.20)

I dont think the charge group should be so big. Can someone suggest what
is going on ?

The input file contains broken molecules. There is nothing wrong, per se,
but only in the case when molecules are split across periodic boundaries.
This is a new check as of version 4.5.

-Justin

Ami

--
==**==

Re: [gmx-users] Re: local pressure v4.5 issues

2011-06-30 Thread Amit Choubey

Hello Everyone,

The git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used
gromacs-4.0.2_localpressure.tar.gzftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file localpressure.dat . On
the contrary in v 4.5 there were separate localpressure.dat* files for
each frame.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote:

On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

May I ask you a question?
In your calculation of local pressure using a trajectory file, did you get
a single averaged localpressure.dat file? Or else you get a bunch of
separate files for each frame (e.g., localpressure.dat0, localpressure.dat1,
localpressure.dat2 )?

Yes I do get different files for different trajectories. All the files seem
to have the same problem ie a very large/small number printed as tensor
elements of the pressure for some of the voxels.

Do you have such problems ? Could we compare our methodologies to use the
local pressure version ?

Amit

Thank you very much!

Cheers,
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Monday, 20 June 2011 07:08:03
*Subject:* [gmx-users] Re: local pressure v4.5 issues

Dear all,

I did another simulation with only SPC water. Then I used the local
pressure gromacs to calculate the stresses. It seems to be reasonable.

I am not sure how to figure out what goes wrong with my previous
simulations when plugged into the local pressure gromacs.

Could someone help me in figuring out whats the issue ?

Thank You.

On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote:

Dear all,

I installed the git version of local pressure calculation from

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

The I invoked mdrun

mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid
0.1

This created a file named localpressure.dat0. This is a binary file so
I could not look at it directly. I am not sure if there is a tool in the
gromacs to look at it directly.

To look at the data in localpressure.dat0 I used the planar_av.c code
available in pressure-tools folder at

http://md.chem.rug.nl/cgmartini/index.php/3d

When I look at the Pressure tensor averaged over xy plane, some of the
numbers are reasonable but few of them are ridiculously large numbers which
is not expected.

I checked this on two different simulations and I got the same problems.
The simulations had run OK previously.

Could someone help me in figuring our whats going on ?

Amit Choubey

Re: [gmx-users] Re: local pressure v4.5 issues

2011-06-30 Thread Amit Choubey

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

In v4.5 it outputs the profile for frames in separate files which is ok. My
concern is what exactly is going in v 4.0 where there is only one file for
all the frames.

Also where did you download v4.5 and v4.0 from ?

Btw, did you use CHARMM FF in your simulations and how did you convert the
tpr files from v 4.5 to v 4.0?

Yes i have used CHARMM FF and i will have to figure out the conversion.

Cheers
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users
gmx-users@gromacs.org
*Sent:* Friday, 1 July 2011 10:32:07
*Subject:* Re: [gmx-users] Re: local pressure v4.5 issues

Hello Everyone,

The git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used
gromacs-4.0.2_localpressure.tar.gzftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file localpressure.dat . On
the contrary in v 4.5 there were separate localpressure.dat* files for
each frame.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote:

On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote:

Hi Amit,

Yes I do get different files for different trajectories. All the files
seem to have the same problem ie a very large/small number printed as tensor
elements of the pressure for some of the voxels.

Do you have such problems ? Could we compare our methodologies to use the
local pressure version ?

Amit

Thank you very much!

Cheers,
Jianguo

--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Monday, 20 June 2011 07:08:03
*Subject:* [gmx-users] Re: local pressure v4.5 issues

Dear all,

I did another simulation with only SPC water. Then I used the local
pressure gromacs to calculate the stresses. It seems to be reasonable.

I am not sure how to figure out what goes wrong with my previous
simulations when plugged into the local pressure gromacs.

Could someone help me in figuring out whats the issue ?

Thank You.

On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.comwrote:

Dear all,

I installed the git version of local pressure calculation from

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

The I invoked mdrun

mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid
0.1

This created a file named localpressure.dat0. This is a binary file so
I could not look at it directly. I am not sure if there is a tool in the
gromacs to look at it directly.

To look at the data in localpressure.dat0 I used the planar_av.c code
available in pressure-tools folder at

http://md.chem.rug.nl/cgmartini/index.php/3d

When I look at the Pressure tensor averaged over xy plane, some of the
numbers are reasonable but few of them are ridiculously large numbers which
is not expected.

I checked this on two different simulations and I got the same problems.
The simulations had run OK previously.

Could someone help me in figuring our whats going on ?

Amit Choubey

[gmx-users] Re: local pressure v4.5 issues

2011-06-19 Thread Amit Choubey

Dear all,

I did another simulation with only SPC water. Then I used the local pressure
gromacs to calculate the stresses. It seems to be reasonable.

I am not sure how to figure out what goes wrong with my previous simulations
when plugged into the local pressure gromacs.

Could someone help me in figuring out whats the issue ?

Thank You.

On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote:

 Dear all,

 I installed the git version of local pressure calculation from


 http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

 The I invoked mdrun

 mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1

 This created a file named localpressure.dat0. This is a binary file so I
 could not look at it directly. I am not sure if there is a tool in the
 gromacs to look at it directly.

 To look at the data in localpressure.dat0 I used the planar_av.c code
 available in pressure-tools folder at

 http://md.chem.rug.nl/cgmartini/index.php/3d

 When I look at the Pressure tensor averaged over xy plane, some of the
 numbers are reasonable but few of them are ridiculously large numbers which
 is not expected.

 I checked this on two different simulations and I got the same problems.
 The simulations had run OK previously.

 Could someone help me in figuring our whats going on ?

 Amit Choubey


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Please search the archive at 
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[gmx-users] local pressure v4.5 issues

2011-06-17 Thread Amit Choubey

Dear all,

I installed the git version of local pressure calculation from

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

The I invoked mdrun

mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1

This created a file named localpressure.dat0. This is a binary file so I
could not look at it directly. I am not sure if there is a tool in the
gromacs to look at it directly.

To look at the data in localpressure.dat0 I used the planar_av.c code
available in pressure-tools folder at

http://md.chem.rug.nl/cgmartini/index.php/3d

When I look at the Pressure tensor averaged over xy plane, some of the
numbers are reasonable but few of them are ridiculously large numbers which
is not expected.

I checked this on two different simulations and I got the same problems. The
simulations had run OK previously.

Could someone help me in figuring our whats going on ?

Amit Choubey
-- 
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] local pressure calcuation for Gromacs-4.5

2011-06-15 Thread Amit Choubey

Dear all,

Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.

Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 15/06/2011 9:09 PM, Jianguo Li wrote:

  Dear all,

 I have made a test calculation of local pressure using version 4.5 for my
 membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives
 the localpressure data. Howeve, instead of giving an anveraged data of the
 local pressure, mdrun gives a separate file for each frame, so I got many
 files: localpressure.dat0, localpressure.dat1, localpressure.dat2,
 localpressure.dat3 ..
 Then I need to calculate the pressure tensor for each frame and make
 average. but these localpressure.dat files are very big (each file is about
 30 Mb), occupying large space of the hard disk. Can anyone give some
 suggestions on how to fix this? Thank you very much!


 I would expect that the output frequency is configurable, but can only
 suggest you consult what documentation exists for this version. Your main
 alternatives are

 * to compress the files with (say) bzip2 or (less effective) gzip and
 construct a script to uncompress them singly and analyse them on the fly
 (AMBER users do a bit of this kind of thing, Google around)
 * to discard ones that are too frequent. However, judging from the numbers
 below, every 100ps is probably OK.

 Mark


  The command is:
 mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
 box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
 And the output message is:
 
 Dumping local pressure based on 1 frames to localpressure.dat0...
 Reading frame   2 time 119400.000

 Dumping local pressure based on 1 frames to localpressure.dat1...
 Reading frame   3 time 119500.000

 Dumping local pressure based on 1 frames to localpressure.dat2...
 Reading frame   4 time 119600.000

 Dumping local pressure based on 1 frames to localpressure.dat3...
 Reading frame   5 time 119700.000

 Dumping local pressure based on 1 frames to localpressure.dat4...
 Reading frame   6 time 119800.000
 ...

 Cheers,
 Jianguo



  --
 *From:* Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 *To:* Discussion list for GROMACS users 
 gmx-users@gromacs.orggmx-users@gromacs.org
 *Sent:* Friday, 10 June 2011 07:10:35
 *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5



 Amit Choubey wrote:
  Thanks Justin, I tried to install the recent git version but the
 configure file is missing. How should I install this version ?
 

 Run the bootstrap script.  It generates the configure script.

 -Justin

 
  On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:
 
 
 
 Amit Choubey wrote:
 
 Dear all,
 
 I saw an unanswered post at
 
 http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
 
 It is about calculating local pressure in v 4.5 when using
 CHARMM FF. Could someone give me some pointers about this?
 
 
 I don't know what the development status of version 4.5 is, but you
 can access it at:
 
 
 http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
 
 It hasn't been merged with release-4-5-patches in some time, so many
 resolved bugs won't be fixed.
 
 -Justin
 
 --
 
 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
 tel:%28540%29%20231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
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 -- 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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[gmx-users] local pressure calcuation for Gromacs-4.5

2011-06-09 Thread Amit Choubey

Dear all,

I saw an unanswered post at

http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

It is about calculating local pressure in v 4.5 when using CHARMM FF. Could
someone give me some pointers about this?

Thank you
Amit
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Re: [gmx-users] local pressure calcuation for Gromacs-4.5

2011-06-09 Thread Amit Choubey

Thanks Justin, I tried to install the recent git version but the configure
file is missing. How should I install this version ?


On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Dear all,

 I saw an unanswered post at
 http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

 It is about calculating local pressure in v 4.5 when using CHARMM FF.
 Could someone give me some pointers about this?


 I don't know what the development status of version 4.5 is, but you can
 access it at:


 http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

 It hasn't been merged with release-4-5-patches in some time, so many
 resolved bugs won't be fixed.

 -Justin

 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
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Re: [gmx-users] Why does the -append option exist?

2011-06-03 Thread Amit Choubey

Well sometimes i run out of walltime when doing long simulations and append
helps me not to do any file management after restarting simulations from the
previous checkpoint.

On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov dpac...@brandeis.edu wrote:


 At first, I thought the -append option of the mdrun command was great.
 However, I don't think it is anymore and have actually  started questioning
 myself why it exists at the first place, and second, why has it become the
 default option in the newest versions?

 It is useless unless you run your simulations in a 100% safe from any
 unexpected problems (hardware, restarts, etc) mode, which is never the case.
 It is beyond me how such an option can become the default and how a
 statement like this:

 By default the output will be appending to the existing output files. The
 checkpoint file contains checksums of all output files, such that *you
 will never loose data when some output files are modified, corrupt or
 removed.*

 can be claimed without testing ALL of the scenarios that can lead to
 problems, that is, lost data.

 If one uses that option and the run is restarted and is again restarted
 before reaching the point of attempting to write a file, then things are
 lost, and most importantly, the most important piece of data, that being the
 trajectory file, could be completely lost! I don't know the code behind the
 checkpointing  appending, but I can see how easy one can overwrite 100ns
 trajectories, for example, and obtain the same trajectories of size 
 0.



Two restarts within a time frame where trajectory file is updated doesnt
make sense. I really dont understand how you can loose trajectory files.


 Using the checkpoint capability  appending make sense when many restarts
 are expected, but unfortunately it is exactly then when these options
 completely fail!


How ?


 As a new user of Gromacs, I must say I am disappointed, and would like to
 obtain an explanation of why the usage of these options is clearly stated to
 be safe when it is not, and why the append option is the default, and why at
 least a single warning has not been posted anywhere in the docs  manuals?


Use -noappend


 Thanks,
 Dimitar




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[gmx-users] saving velocities and coordinates frequently

2011-02-17 Thread Amit Choubey

Hi ,

I wish to save velocities and coordinates every step for my system. For
saving disk space i dont want to save water molecules. How can i do this ?

Amit
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Re: [gmx-users] Energy minimization

2011-01-17 Thread Amit Choubey

Can you provide more details ? Which graph are you talking about ?

Amit

On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta bharat.85.m...@gmail.comwrote:

 Hi all,

 I am minimizing my protein (230 amino acids)  with the minim.mdp file given
 in the lysozyme tutorial but I am not getting a stable graph .. I checked
 the manual also to look for parameters but I am not able to find such
 information there apart from the theory about the minimzation algos and
 process.. So can anybody direct me to some relevant link or help me out in
 this regard ??



 --
 Bharat
 Ph.D. Candidate
 Room No. : 7202A, 2nd Floor
 Biomolecular Engineering Laboratory
 Division of Chemical Engineering and Polymer Science
 Pusan National University
 Busan -609735
 South Korea
 Lab phone no. - +82-51-510-3680, +82-51-583-8343
 Mobile no. - 010-5818-3680
 E-mail : monu46...@yahoo.com


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Re: [gmx-users] Energy minimization

2011-01-17 Thread Amit Choubey

OK what seemed wrong to you?

On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta bharat.85.m...@gmail.comwrote:

 I am doin the first minimization step.. here are the details of minim.mdp
 file

 ; minim.mdp - used as input into grompp to generate em.tpr
 ; Parameters describing what to do, when to stop and what to save
 integrator = steep  ; Algorithm (steep = steepest descent minimization)
 emtol  = 1000.0   ; Stop minimization when the maximum force  1000.0
 kJ/mol/nm
 emstep  = 0.01  ; Energy step size
 nsteps  = 5; Maximum number of (minimization) steps to perform
 ; Parameters describing how to find the neighbors of each atom and how to
 calculate the interactions
 nstlist  = 1  ; Frequency to update the neighbor list and long range forces
 ns_type  = grid  ; Method to determine neighbor list (simple, grid)
 rlist  = 1.0  ; Cut-off for making neighbor list (short range forces)
 coulombtype = PME  ; Treatment of long range electrostatic interactions
 rcoulomb = 1.0  ; Short-range electrostatic cut-off
 rvdw  = 1.0  ; Short-range Van der Waals cut-off
 pbc  = xyz   ; Periodic Boundary Conditions (yes/no)



 --
 Bharat
 Ph.D. Candidate
 Room No. : 7202A, 2nd Floor
 Biomolecular Engineering Laboratory
 Division of Chemical Engineering and Polymer Science
 Pusan National University
 Busan -609735
 South Korea
 Lab phone no. - +82-51-510-3680, +82-51-583-8343
 Mobile no. - 010-5818-3680
 E-mail : monu46...@yahoo.com


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Re: [gmx-users] Energy minimization

2011-01-17 Thread Amit Choubey

Check your log file to see if the minimization criterion was satisfied ie
the max force is less than emtol.

On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta bharat.85.m...@gmail.comwrote:


 The potential energy graph is not coming parallel to x-axis is getting down
 towars the x-axis .. normally it should be paralle to x-axis..

 --
 Bharat
 Ph.D. Candidate
 Room No. : 7202A, 2nd Floor
 Biomolecular Engineering Laboratory
 Division of Chemical Engineering and Polymer Science
 Pusan National University
 Busan -609735
 South Korea
 Lab phone no. - +82-51-510-3680, +82-51-583-8343
 Mobile no. - 010-5818-3680
 E-mail : monu46...@yahoo.com


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[gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

Hi all,

I am trying to do pulling simulation. Following are the pull parameters

pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes

Everything works fine until the pull group COM reaches half the box length.
The COM position changes by the box length and that causes huge force on the
group. What should i do to fix this ? Also i am using NPT coupling.

Amit
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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

Hi,

Initially, the pull group center of mass is at 8.16 nm and i want to pull 15
nm. I started with a box size of 37 nm in the pull direction.

The problem occurs when the COM is at 18.5 nm (ie at half the box length).

Thanks for the attention.

Amit

On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi all,

 I am trying to do pulling simulation. Following are the pull parameters

 pull = umbrella
 pull_geometry = direction
 pull_vec1 = 0 0 1
 pull_group1 = RNA
 pull_rate1 = 0.01
 pull_k1 = 1000
 pull_start = yes

 Everything works fine until the pull group COM reaches half the box
 length. The COM position changes by the box length and that causes huge
 force on the group. What should i do to fix this ? Also i am using NPT
 coupling.


 You have to use a sufficiently large box, otherwise the periodic distance
 becomes the reference distance when this happens.  This has been discussed
 numerous times on the list (hint: there is an archive for a reason!) and in
 the tutorial linked here:


 http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

 -Justin

  Amit


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

Hi,

I am still not able to see the reason for the periodic distances coming into
picture.

Also, why pull_geometry = direction_periodic cannot be used with P-coupling;
although it seems to do what i want.

Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi,

 Initially, the pull group center of mass is at 8.16 nm and i want to pull
 15 nm. I started with a box size of 37 nm in the pull direction.

 The problem occurs when the COM is at 18.5 nm (ie at half the box length).

 Thanks for the attention.

 Amit

 On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul jalem...@vt.eduwrote:



 Amit Choubey wrote:

 Hi all,

 I am trying to do pulling simulation. Following are the pull parameters

 pull = umbrella
 pull_geometry = direction
 pull_vec1 = 0 0 1
 pull_group1 = RNA
 pull_rate1 = 0.01
 pull_k1 = 1000
 pull_start = yes

 Everything works fine until the pull group COM reaches half the box
 length. The COM position changes by the box length and that causes huge
 force on the group. What should i do to fix this ? Also i am using NPT
 coupling.


 You have to use a sufficiently large box, otherwise the periodic distance
 becomes the reference distance when this happens.  This has been discussed
 numerous times on the list (hint: there is an archive for a reason!) and in
 the tutorial linked here:


 http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

 -Justin

  Amit


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
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 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

Yes Justin i understand that. Heres what i think is going on

I dont have any reference group. Now the COM distance is calculated wrt the
origin and whenever the COM is more than half of the box its causing
problem.

I think changing the absolute reference to the initial COM of the pull group
(using pull_init1) should fix this issue but i am not confident.

Thanks for looking into this.

On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi,
 I am still not able to see the reason for the periodic distances coming
 into picture.


 I guess I don't fully understand your procedure.  If you only want to pull
 to a COM separation of 15 nm, there should be no problem, but yet you're
 achieving a COM separation of 18.5 nm?  That's exactly the problem.  If your
 box is 37 nm, 18.5 nm corresponds to the transition at which the code
 utilizes either the unit cell distance or the periodic distance as the
 restraint distance.  So it is as this point that your forces go haywire.

 -Justin

  Also, why pull_geometry = direction_periodic cannot be used with
 P-coupling; although it seems to do what i want.

 Amit

 On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey kgp.a...@gmail.commailto:
 kgp.a...@gmail.com wrote:

Hi,

Initially, the pull group center of mass is at 8.16 nm and i want to
pull 15 nm. I started with a box size of 37 nm in the pull direction.
The problem occurs when the COM is at 18.5 nm (ie at half the box
length).

Thanks for the attention.

Amit

On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:



Amit Choubey wrote:

Hi all,

I am trying to do pulling simulation. Following are the pull
parameters

pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes

Everything works fine until the pull group COM reaches half
the box length. The COM position changes by the box length
and that causes huge force on the group. What should i do to
fix this ? Also i am using NPT coupling.


You have to use a sufficiently large box, otherwise the periodic
distance becomes the reference distance when this happens.  This
has been discussed numerous times on the list (hint: there is an
archive for a reason!) and in the tutorial linked here:


 http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-Justin

Amit


-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).

Amit

On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Yes Justin i understand that. Heres what i think is going on

 I dont have any reference group. Now the COM distance is calculated wrt
 the origin and whenever the COM is more than half of the box its causing
 problem.


 Correct.


  I think changing the absolute reference to the initial COM of the pull
 group (using pull_init1) should fix this issue but i am not confident.


 Using a defined reference group is the better method.  That way, the pull
 distance is calculated with respect to this reference, and it sounds like
 that will allow you to use the box you have already set up.

 -Justin

  Thanks for looking into this.

 On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:

Hi,

I am still not able to see the reason for the periodic distances
coming into picture.


I guess I don't fully understand your procedure.  If you only want
to pull to a COM separation of 15 nm, there should be no problem,
but yet you're achieving a COM separation of 18.5 nm?  That's
exactly the problem.  If your box is 37 nm, 18.5 nm corresponds to
the transition at which the code utilizes either the unit cell
distance or the periodic distance as the restraint distance.  So it
is as this point that your forces go haywire.

-Justin

Also, why pull_geometry = direction_periodic cannot be used with
P-coupling; although it seems to do what i want.

Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
kgp.a...@gmail.com mailto:kgp.a...@gmail.com
mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote:

   Hi,

   Initially, the pull group center of mass is at 8.16 nm and i
want to
   pull 15 nm. I started with a box size of 37 nm in the pull
direction.
   The problem occurs when the COM is at 18.5 nm (ie at half the
 box
   length).

   Thanks for the attention.

   Amit

   On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
   mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Amit Choubey wrote:

   Hi all,

   I am trying to do pulling simulation. Following are
the pull
   parameters

   pull = umbrella
   pull_geometry = direction
   pull_vec1 = 0 0 1
   pull_group1 = RNA
   pull_rate1 = 0.01
   pull_k1 = 1000
   pull_start = yes

   Everything works fine until the pull group COM
reaches half
   the box length. The COM position changes by the box
length
   and that causes huge force on the group. What should
i do to
   fix this ? Also i am using NPT coupling.


   You have to use a sufficiently large box, otherwise the
periodic
   distance becomes the reference distance when this
happens.  This
   has been discussed numerous times on the list (hint:
there is an
   archive for a reason!) and in the tutorial linked here:


 http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

   -Justin

   Amit


   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu http://vt.edu |

(540) 231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

2011-01-07 Thread Amit Choubey

try the -type option with dihedral

amit

On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous carlajam...@gmail.com wrote:

 Hi Everyone,

 Please I'm trying to calculate one dihedral angle as a function of time
 during my simulation.
 For this, I used g_angle. In the manual (version 4.0.3) it says: the
 indexfile should contain atom-triplets or atom-quadruplets for dihedrals.

 I put an atom-quadruplet in my index file, but when I run
 g_angle -f .xtc -n .ndx -od .xvg

 and I select the group of atom-quadruplets, gromacs crashes and shows this
 error message:
 number of index elements not multiple of 3, these can not be angle triplets

 So actually g_angle only calculates angles not dihedrals?

 Thanks

 Carla


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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

2011-01-07 Thread Amit Choubey

Yes -ov does give you average angle as a function of time. I am not sure if
this answers your question though.

amit

On Fri, Jan 7, 2011 at 2:40 AM, Carla Jamous carlajam...@gmail.com wrote:

 Thank you,

 It worked, one last question. Something is not very clear to me:

 -ov: plots the average angle of a group of angles as a function of time!!
 What does it mean?

 Because I'm getting positive and negative values in the same plot. Are
 these values the values of my dihedral angle as a function of time?

 Thanks again,
 Carla


 On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey kgp.a...@gmail.com wrote:

 try the -type option with dihedral

 amit

 On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous carlajam...@gmail.comwrote:

 Hi Everyone,

 Please I'm trying to calculate one dihedral angle as a function of time
 during my simulation.
 For this, I used g_angle. In the manual (version 4.0.3) it says: the
 indexfile should contain atom-triplets or atom-quadruplets for dihedrals.

 I put an atom-quadruplet in my index file, but when I run
 g_angle -f .xtc -n .ndx -od .xvg

 and I select the group of atom-quadruplets, gromacs crashes and shows
 this error message:
 number of index elements not multiple of 3, these can not be angle
 triplets

 So actually g_angle only calculates angles not dihedrals?

 Thanks

 Carla


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Re: [gmx-users] trjconv with multiple chains

2011-01-07 Thread Amit Choubey

Make your box bigger?

2011/1/6 yuanyuan wang yilin3...@126.com

 dear all,
  I am doing a simulation that have many chains in a box , and I can
 find a center for them after serval tries.
  I use almost every option of trjconv,-pbc
 mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box,
 and -boxcenter, -fit ..
  still some chain cannot convert into box. them jump from one box
 to another ,
  is there any ways that they not jump to another box?
  thanks a lot.


 yuanyuan



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Re: [gmx-users] so difficult problem

2011-01-04 Thread Amit Choubey

There is something wrong with your initial configuration. May be you forgot
to take care of periodicity, how did you get your initial configuration?
Also notice that these kind of problems have been discussed previously.

Amit

On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour 
ramezanpour.moh...@gmail.com wrote:

 Dear All
 I am using this .mdp file and I recived the below warnings,I can't solve
 that.


 title= NPT
 define   =
 integrator   = md
 tinit= 0
 dt   = 0.002
 nsteps   = 50
 nstcomm  = 1
 comm-grps= protein non-protein
 niter= 20
 nstxout  = 5000
 nstvout  = 5000
 nstfout  = 0
 nstlog   = 5000
 nstenergy= 250
 nstxtcout= 250
 xtc-precision= 1000
 xtc_grps = protein non-protein
 energygrps   = Protein  non-protein
 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4
 domain-decomposition = no
 coulombtype  = PME
 rcoulomb-switch  = 0
 rcoulomb = 1.4
 epsilon-r= 1
 vdw-type = Cut-off
 rvdw-switch  = 0
 rvdw = 1.4
 DispCorr = EnerPres
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 ewald_rtol   = 1e-05
 epsilon_surface  = 0
 optimize_fft = no
 tcoupl   = Nose-hoover
 tc-grps  = Protein non-protein
 tau_t= 0.1  0.1
 ref_t= 300  300
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = Isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 annealing= no
 gen_vel  = yes
 gen_temp = 310
 gen_seed = 173529
 constraints  = all-bonds
 constraint-algorithm = Lincs
 unconstrained-start  = no
 lincs-order  = 4
 lincs-warnangle  = 30
 morse= no

 my sytem is protein-ligand,I want to generate a NPT.
 the result was:

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 starting mdrun 'Protein in water'
 50 steps,   1000.0 ps.

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
5264   5263   41.70.1143   0.1261  0.1140
5293   5294   82.70.1221 2612.9744  0.1090
5291   5293   77.20.1517 6082.6147  0.1390
5291   5292  101.00.1117 1518.6106  0.1090
5289   5291   87.70.1353 6891.8911  0.1390
5289   5290   88.40.1437 7529.4878  0.1360
5289   5287   88.40.1456 7540.4873  0.1390
5287   5288   89.70.1092 381.5114  0.1090
5285   5287   92.30.1395 354.9220  0.1390
5285   5286  123.80.1101  44.8448  0.1090
5284   5293   89.00.1478 4605.1763  0.1390
5284   5285   79.30.1402 173.5627  0.1390
5278   5279   78.90.1529   1.1270  0.1530
5277   5278  122.90.1545  13.1423  0.1530
5276   5284   84.90.1422 159.0098  0.1390
5276   5277   68.40.1543  90.8248  0.1530
5276   5275   39.50.1439  72.5216  0.1430
5274   5275  103.70.1436  21.6028  0.1430
5273   5274  108.50.1394   3.3421  0.1390
5276   5272   45.70.1402  80.6795  0.1390
5272   5273  127.30.1340  14.2401  0.1330
5272   5270   69.80.1336  12.6250  0.1330
5270   5271  113.30.1092   0.2530  0.1090
5268   5270  104.60.1391   0.2718  0.1390
5268   5269   44.40.1091   0.1636  0.1090
5273   5266   58.50.1342  14.0125  0.1330
5265   5268   36.50.1394   0.1769  0.1390

 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

 Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
 Wrote pdb files with previous and current coordinates
 step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965
 which is larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 Please let me know the solution.

Re: [gmx-users] so difficult problem

2011-01-04 Thread Amit Choubey

May be you broke the molecule while using editconf. Try to fix the
periodicity by trjconv and then use it.

On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour 
ramezanpour.moh...@gmail.com wrote:

 I generated my .top and .gro file as drug/enzyme tutorial.
 I used PRODRG to generate them.
 I could pass all of steps in UMbrella sampling tutorial with these
 files,without any warning or error.
 the one thing I changed is rotating box with editconf.




 On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.com wrote:

 There is something wrong with your initial configuration. May be you
 forgot to take care of periodicity, how did you get your initial
 configuration? Also notice that these kind of problems have been discussed
 previously.

 Amit

 On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour 
 ramezanpour.moh...@gmail.com wrote:

 Dear All
 I am using this .mdp file and I recived the below warnings,I can't solve
 that.


 title= NPT
 define   =
 integrator   = md
 tinit= 0
 dt   = 0.002
 nsteps   = 50
 nstcomm  = 1
 comm-grps= protein non-protein
 niter= 20
 nstxout  = 5000
 nstvout  = 5000
 nstfout  = 0
 nstlog   = 5000
 nstenergy= 250
 nstxtcout= 250
 xtc-precision= 1000
 xtc_grps = protein non-protein
 energygrps   = Protein  non-protein
 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4
 domain-decomposition = no
 coulombtype  = PME
 rcoulomb-switch  = 0
 rcoulomb = 1.4
 epsilon-r= 1
 vdw-type = Cut-off
 rvdw-switch  = 0
 rvdw = 1.4
 DispCorr = EnerPres
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 ewald_rtol   = 1e-05
 epsilon_surface  = 0
 optimize_fft = no
 tcoupl   = Nose-hoover
 tc-grps  = Protein non-protein
 tau_t= 0.1  0.1
 ref_t= 300  300
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = Isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 annealing= no
 gen_vel  = yes
 gen_temp = 310
 gen_seed = 173529
 constraints  = all-bonds
 constraint-algorithm = Lincs
 unconstrained-start  = no
 lincs-order  = 4
 lincs-warnangle  = 30
 morse= no

 my sytem is protein-ligand,I want to generate a NPT.
 the result was:

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 starting mdrun 'Protein in water'
 50 steps,   1000.0 ps.

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
5264   5263   41.70.1143   0.1261  0.1140
5293   5294   82.70.1221 2612.9744  0.1090
5291   5293   77.20.1517 6082.6147  0.1390
5291   5292  101.00.1117 1518.6106  0.1090
5289   5291   87.70.1353 6891.8911  0.1390
5289   5290   88.40.1437 7529.4878  0.1360
5289   5287   88.40.1456 7540.4873  0.1390
5287   5288   89.70.1092 381.5114  0.1090
5285   5287   92.30.1395 354.9220  0.1390
5285   5286  123.80.1101  44.8448  0.1090
5284   5293   89.00.1478 4605.1763  0.1390
5284   5285   79.30.1402 173.5627  0.1390
5278   5279   78.90.1529   1.1270  0.1530
5277   5278  122.90.1545  13.1423  0.1530
5276   5284   84.90.1422 159.0098  0.1390
5276   5277   68.40.1543  90.8248  0.1530
5276   5275   39.50.1439  72.5216  0.1430
5274   5275  103.70.1436  21.6028  0.1430
5273   5274  108.50.1394   3.3421  0.1390
5276   5272   45.70.1402  80.6795  0.1390
5272   5273  127.30.1340  14.2401  0.1330
5272   5270   69.80.1336  12.6250  0.1330
5270   5271  113.30.1092   0.2530  0.1090
5268   5270  104.60.1391   0.2718  0.1390
5268   5269   44.40.1091   0.1636  0.1090
5273   5266   58.50.1342  14.0125  0.1330
5265   5268   36.50.1394   0.1769  0.1390

Re: [gmx-users] so difficult problem

2011-01-04 Thread Amit Choubey

Could you post the exact command lines ?

On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour 
ramezanpour.moh...@gmail.com wrote:

 please let me know more.
 I am new with gromacs.
 did I understand correctly?You say me to use from trjconv at first and then
 from editconf?
  I want to keep fix my molecule and rotate my box to locate in awanted
 direction.
 waht can I do?
 because when I rotate the box my molecule totally is located out of box,but
 protein and ligand are connected as the first state and I think my molecule
 has not broken.
 Thanks in advance


 On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey kgp.a...@gmail.com wrote:

 May be you broke the molecule while using editconf. Try to fix the
 periodicity by trjconv and then use it.


 On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour 
 ramezanpour.moh...@gmail.com wrote:

 I generated my .top and .gro file as drug/enzyme tutorial.
 I used PRODRG to generate them.
 I could pass all of steps in UMbrella sampling tutorial with these
 files,without any warning or error.
 the one thing I changed is rotating box with editconf.




 On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.comwrote:

 There is something wrong with your initial configuration. May be you
 forgot to take care of periodicity, how did you get your initial
 configuration? Also notice that these kind of problems have been discussed
 previously.

 Amit

 On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour 
 ramezanpour.moh...@gmail.com wrote:

 Dear All
 I am using this .mdp file and I recived the below warnings,I can't
 solve that.


 title= NPT
 define   =
 integrator   = md
 tinit= 0
 dt   = 0.002
 nsteps   = 50
 nstcomm  = 1
 comm-grps= protein non-protein
 niter= 20
 nstxout  = 5000
 nstvout  = 5000
 nstfout  = 0
 nstlog   = 5000
 nstenergy= 250
 nstxtcout= 250
 xtc-precision= 1000
 xtc_grps = protein non-protein
 energygrps   = Protein  non-protein
 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4
 domain-decomposition = no
 coulombtype  = PME
 rcoulomb-switch  = 0
 rcoulomb = 1.4
 epsilon-r= 1
 vdw-type = Cut-off
 rvdw-switch  = 0
 rvdw = 1.4
 DispCorr = EnerPres
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 ewald_rtol   = 1e-05
 epsilon_surface  = 0
 optimize_fft = no
 tcoupl   = Nose-hoover
 tc-grps  = Protein non-protein
 tau_t= 0.1  0.1
 ref_t= 300  300
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = Isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 annealing= no
 gen_vel  = yes
 gen_temp = 310
 gen_seed = 173529
 constraints  = all-bonds
 constraint-algorithm = Lincs
 unconstrained-start  = no
 lincs-order  = 4
 lincs-warnangle  = 30
 morse= no

 my sytem is protein-ligand,I want to generate a NPT.
 the result was:

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 starting mdrun 'Protein in water'
 50 steps,   1000.0 ps.

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
5264   5263   41.70.1143   0.1261  0.1140
5293   5294   82.70.1221 2612.9744  0.1090
5291   5293   77.20.1517 6082.6147  0.1390
5291   5292  101.00.1117 1518.6106  0.1090
5289   5291   87.70.1353 6891.8911  0.1390
5289   5290   88.40.1437 7529.4878  0.1360
5289   5287   88.40.1456 7540.4873  0.1390
5287   5288   89.70.1092 381.5114  0.1090
5285   5287   92.30.1395 354.9220  0.1390
5285   5286  123.80.1101  44.8448  0.1090
5284   5293   89.00.1478 4605.1763  0.1390
5284   5285   79.30.1402 173.5627  0.1390
5278   5279   78.90.1529   1.1270  0.1530
5277   5278  122.90.1545  13.1423  0.1530
5276   5284   84.90.1422 159.0098  0.1390

Re: [gmx-users] Signal: Segmentation faul

2011-01-02 Thread Amit Choubey

Your log file does indicate that the steepest descent converged. I dont know
why you have the error messages. Why not go ahead with MD ?

Amit

On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal shikhaiiit...@gmail.comwrote:

 hi,
 HAPPY NEW YEAR

 I am experiencing a segmentation fault during mdrun in equlibration step .
 error

 Wrote pdb files with previous and current coordinates
 [shikha-desktop:01719] *** Process received signal ***
 [shikha-desktop:01719] Signal: Segmentation fault (11)
 [shikha-desktop:01719] Signal code: Address not mapped (1)
 [shikha-desktop:01719] Failing at address: 0x8d22a70
 [shikha-desktop:01719] [ 0] [0xb87410]
 [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]
 [shikha-desktop:01719] *** End of error message ***
 Segmentation fault





 bottom lines of my .log file after energy minimization is this



  Step   Time Lambda
   1135711357.00.0

Step   Time Lambda
   1135811358.00.0

Step   Time Lambda
   1135911359.00.0

Step   Time Lambda
   1136011360.00.0

Step   Time Lambda
   1136111361.00.0


 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  1000

 Double precision normally gives you higher accuracy.
 You might need to increase your constraint accuracy, or turn
 off constraints alltogether (set constraints = none in mdp file)

 Steepest Descents converged to machine precision in 11362 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  = -5.4871900e+06
 Maximum force =  3.9830833e+03 on atom 4511
 Norm of force =  1.9521437e+01

 M E G A - F L O P S   A C C O U N T I N G

RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
NF=No Forces

  Computing:   M-Number M-Flops  % Flops

 -
  LJ   10523.695513  347281.952 0.4
  Coul(T)   6405.625131  269036.256 0.3
  Coul(T) [W3]   226.446553   28305.819 0.0
  Coul(T) + LJ  4637.739866  255075.693 0.3
  Coul(T) + LJ [W3] 1706.661036  235519.223 0.3
  Coul(T) + LJ [W3-W3]141595.84421154089612.48969.1
  Outer nonbonded loop 18947.604080  189476.041 0.2
  1,4 nonbonded interactions 105.1893969467.046 0.0
  Calc Weights 11755.000218  423180.008 0.5
  Spread Q Bspline250773.337984  501546.676 0.6
  Gather F Bspline250773.337984 1504640.028 1.9
  3D-FFT 1217431.505524 9739452.04412.4
  Solve PME14842.953216  949949.006 1.2
  NS-Pairs418574.562328 8790065.80911.2
  Reset In Box  1338.8867184016.660 0.0
  Shift-X   3916.765450   23500.593 0.0
  CG-CoM3918.333406   11755.000 0.0
  Bonds  114.1312906733.746 0.0
  Angles 142.695358   23972.820 0.0
  Propers102.167104   23396.267 0.0
  Impropers   28.9844626028.768 0.0
  RB-Dihedrals 2.885948 712.829 0.0
  Pos. Restr. 38.1990441909.952 0.0
  Virial3918.844696   70539.205 0.1
  Settle2534.725856  818716.451 1.0

 -
  Total78323890.379   100.0

 -


  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

  Computing: Nodes Number G-CyclesSeconds %
 ---
  Neighbor search1  1136230337.457 6067.718.8
  Force  1  1136235859.263 7172.122.3
  PME mesh   1  1136212486.060 2497.3 7.8
  Constraints1  22723 1294.000  258.8 0.8
  Rest   1   81096.73016219.850.3
 ---

Re: [gmx-users] CMAP error

2010-12-09 Thread Amit Choubey

This may not be related but it was not straight forward to do DPPC membrane
simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at
all in the FF files.

The DPPC is defined in terms of two more residues in CHARMM.

amit

On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Jon Mujika wrote:

 Dear all,

 I am setting up a system with GROMACS 4.5.3 and the CHARMM force
 field. In the protein, I have a neutral lysine, for which CHARMM force
 filed has a specific residue type (LSN). When I wrote LSN as residue
 name in the initial pdb file, the topology file was perfectly created
 by pdb2gmx. However, in the next step, grompp complained about the
 CMAP torsion between the two previous residues:

 Fatal error:
 Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

 However, if the LYS residue was written in the initial pdb file and
 the -lys option included with pdb2gmx (chosen the neutral protonation
 state for this lysine), grompp did not complain.

 The problem is that there is a deprotonated tyrosine (bound to a
 metal) in my system. I created a new residue type, but again the
 grompp complained about the CMAP between the two previous residues.
 Unfortunately, in this case I can't fit the problem with any of the
 pdb2gms options.
 I think the problem arises when a non-standard residue is included in
 the initial pdb file. Does someone else find this problem? I would
 appreciate any advise about how to solve it.


 I can't promise a solution, but you could try adding LSN and whatever other
 non-standard residues you need to use in residuetypes.dat.  I noticed that
 LSN is not there, which seems like an omission, since the other
 CHARMM-specific residue names are there.  When LYS is present, probably
 pdb2gmx is correctly interpreting the residue as protein before converting
 its name.  In the case of LSN or any other non-standard residue, this may
 not be the case.  Check the output of pdb2gmx carefully for any messages
 that might indicate that a residue of type Other was detected.  I've had
 this cause other problems.

 If adding LSN to residuetypes.dat fixes the problem, I will file a
 bugzilla.

 -Justin

  Thanks in advance

 Jon


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 

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Re: [gmx-users] Hard Spheres

2010-12-08 Thread Amit Choubey

On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel 
sascha.hem...@bci.tu-dortmund.de wrote:

 Hi all!

 I am trying to add some hard spheres to my simulation. As far as i can
 tell from the manual Gromacs supports only LJ or Buckingham for
 non-bonded interaction.


Why cant you use  LJ? By setting the attractive part equal to zero.



 Is there a way to add hard spheres to lets say a simulation of Water
 molecules without interfering into the regular water-water interaction?

 Thanks a lot in advance,

 Sascha

 TU Dortmund
 Laboratory of Thermodynamics
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Re: [gmx-users] -symm option

2010-12-08 Thread Amit Choubey

try using to find out, its described on
http://manual.gromacs.org/current/online/g_density.html

On Wed, Dec 8, 2010 at 4:10 AM, Morteza Khabiri khab...@greentech.czwrote:

 Dear all

 does somebody knows how -symm option from g_density command do the
 calculations?
 Or in other word what is the basic of -symm option?

 Thanks



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Re: [gmx-users] dna, lipid simulation

2010-12-05 Thread Amit Choubey

Thank you all. At least now I have an idea of the starting point.

On Sun, Dec 5, 2010 at 12:31 PM, Thomas Piggot t.pig...@soton.ac.uk wrote:

  I would tend to agree with Justin rather than Itamar. The GROMOS DNA
 parameters are not especially good (see
 http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you
 are wanting to look at. Another option (rather than CHARMM, which for what
 it is worth is the force field I would probably use) is you could use one of
 the AMBER forcefields for the DNA and the GAFF lipids (although I forget if
 there is DPPC available or not, I think the only fully saturated lipid
 already available might be DMPC), but keep in mind you need to use surface
 tension with these lipids. As I said the choice really depends on what you
 want to look at, so some reading of the literature and also seeing what
 other people have done for similar simulations should help.

 Cheers

 Tom


 On 05/12/10 12:42, Itamar Kass (Med) wrote:

 Hi Amit,

 The GROMOS force field had both DNA and lipids parameters, hence you can
 use it in your simulations. Moreover, there are new lipids parameters by
 David Poger and Alan Mark which I should give better results compared to the
 old set.

 Good luck.


 On 5 December 2010 18:09, Amit Choubey kgp.a...@gmail.com wrote:

 Hi all,

  This is a question unrelated to gromacs but would pose it anyway to get
 some hints from the experts.
 I wish to set up DNA and DPPC lipid membrane simulation. Could someone
 please refer to a relevant forcefield/tutorial for simulation of lipids with
 DNA?

  Any help will be really appreciated.

  Thank you
 amit

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 --

 --


 In theory, there is no difference between theory and practice. But, in
 practice, there is. - Jan L.A. van de Snepscheut

 ===
 | Itamar Kass, Ph.D.
 | Postdoctoral Research Fellow
 |
 | Department of Biochemistry and Molecular Biology
 | Building 77 Clayton Campus
 | Wellington Road
 | Monash University,
 | Victoria 3800
 | Australia
 |
 | Tel: +61 3 9902 9376
 | Fax: +61 3 9902 9500
 | E-mail: itamar.k...@monash.edu
 


 --
 Dr Thomas Piggot
 University of Southampton, UK.


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[gmx-users] dna, lipid simulation

2010-12-04 Thread Amit Choubey

Hi all,

This is a question unrelated to gromacs but would pose it anyway to get some
hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could someone
please refer to a relevant forcefield/tutorial for simulation of lipids with
DNA?

Any help will be really appreciated.

Thank you
amit
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Re: [gmx-users] request

2010-11-21 Thread Amit Choubey

Hi,

Define an itp file which has the non-bonded info. Then define a mdp (md
parameter file) and also make a structure file (gro). Also you need a
topology file (top) which corresponds to the structure file.

You will have to do some background work. Manual should be your friend.

amit

On Sat, Nov 20, 2010 at 11:32 PM, leila separdar
separdar.le...@gmail.comwrote:

 I am beginner with gromacs. I would like to simulate the behavior of glassy
 materials starting with simple Lennard Jones liquid.
 please advise me as to how to begin.
 a relevent flowchart or tutorial would be of immerse help
 thank you very much indeed.

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[gmx-users] question on KALP-15 in DPPC tutorial

2010-11-21 Thread Amit Choubey

Hi all,

I was going through the very nicely presented tutorial by Justin (on KALP-15
in DPPC). I have one question regarding the non-bonded cut-offs. It seems
that people use many different values of non-bonded cut-off (varying from
0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values
for my simulations ?

amit
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Re: [gmx-users] question on KALP-15 in DPPC tutorial

2010-11-21 Thread Amit Choubey

Thank you Mark and Justin. Yes i did check the reference of your tutorial,
but its just that there are so many groups using same FF but different
cut-off lengths.

amit

On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul jalem...@vt.edu wrote:

 Quoting Mark Abraham mark.abra...@anu.edu.au:

  On 21/11/2010 8:45 PM, Amit Choubey wrote:
   Hi all,
  
   I was going through the very nicely presented tutorial by Justin (on
   KALP-15 in DPPC). I have one question regarding the non-bonded
   cut-offs. It seems that people use many different values of non-bonded
   cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i
   choose the cut-off values for my simulations ?
 
  In the first instance, by reproducing the conditions under which the
  parameters were validated. Unfortunately, most of the force fields were
  not parametrized for PME, under which they are often now used. So look
  at some papers from large well-known groups that have done something
  similar to what you want to do, judge how well they have worked, and do
  something comparable. Unfortunately, there have been little or no
  systematic studies of how accurate forcefield X plus PME needs to be to
  model reality usefully. Hopefully that will change :-)
 

 And directly related to the tutorial in question, the settings used therein
 were
 assigned to reproduce the study that I cite in the introductory material.

 -Justin

 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] defining a 3 body user defined potential

2010-10-25 Thread Amit Choubey

Thank you very much for the input Ivan.

On Mon, Oct 25, 2010 at 5:46 AM, Ivan Gladich iglad...@purdue.edu wrote:

 Dear Amit
 As far as I know, 3-body interaction potential is not defined in
 gromacs. If you want to introduce it in Gromacs, you have to change the
 source code. It is not easy but not impossible and it was already done
 for TIP4P, see Kumar and Skinner, J. Phys. Chem. B, 112,8311-8318, 2008

 I hope this help
 Ivan

 Amit Choubey wrote:
  Hi all,
 
  I was wondering if there is a way to define user defined potential which
  involves 3 particles. Thank you for any input.
 
 
  Amit
 
 


 --
 ---
 Ivan Gladich, Ph.D.

 Dreyfus Postdoctoral Fellow
 Department of Chemistry
 Purdue University
 560 Oval Drive, box 140
 West Lafayette
 IN 47906 USA

 Room: 265C
 Tel:765-494-5225
 e-mail: iglad...@purdue.edu
 web page: http://web.ics.purdue.edu/~igladich/

 
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[gmx-users] defining a 3 body user defined potential

2010-10-24 Thread Amit Choubey

Hi all,

I was wondering if there is a way to define user defined potential which
involves 3 particles. Thank you for any input.


Amit
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Re: [gmx-users] GROMACS-4.5-beta1 is out!

2010-07-31 Thread Amit Choubey

Hi Rossen,

Could you send me a documentation of memory usage by gromacs-4.5-beta1. I
would like to know the maximum no. of atoms that we can simulate on our
university supercomputer.

amit

On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov 
rossen.aposto...@cbr.su.se wrote:


 After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is
 out!

 It is full of many new and exciting features, please try them out!

 If something is not working as expected, please send a mail or file a
 bugzilla report.

 For developers: there is a new branch for stable releases called
 release-4-5-patches. Bugfixes should be applied there **first**, and if
 needed, merged from that branch into the master after the fix. See
 http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more
 information.


 New features:

- 2D decomposition support for PME: improved load balancing with up to
40% overall performance improvement for large systems.
- Memory usage is improved for very large systems, allowing simulations
of 100 million atoms.
- Running on multi-core nodes now automatically uses threads for domain
decomposition through the built-in threaded MPI library
- GPU computing support
- Check-pointing is made more secure:MD5sum are used to verify that all
files are correctly in-place before a simulation is appended. Output file
appending at continuation is turned on by default
- Full Cmake support. Autoconf/automake will be deprecated after the
final 4.5 release!
- Full support for 7 AMBER force fields
- Support for CHARMM27, including cmap for dihedrals
- Efficient Generalized-Born implicit solvent support including the
Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating
the generalized Born-interaction formula for greater speed, and optimized
SSE-routines for both cut-off and all-vs-all simulations.
- Support for nucleic acid simulations
- Support for Velocity-Verlet integrators for reversible T- and
P-coupling; MTTK pressure control integrators; Nose-Hoover chains
- Support for Bennett acceptance ratio (BAR) free energy calculations
- Decoupling group setup for free energy
- File formats: All GROMACS tools can now read any VMD supported
trajectory format, without converting trajectory first. (VMD is required)
- g_rdf was a little bit enhanced that structure factors can be
calculated for any system, by supplying the necessary data via sfactor.dat.
Most of the common atomtypes are already contained, but everybody who needs
more freedom can enhance the table
- Library support for dynamic index groups based on textual
selections (experimental feature). See the tool g_select, the included
template.c, or Doxygen documentation for information on how to write
analysis tools using the library. Existing tools have not (yet) been
converted.
- g_tune_pme: For a given number of processes or threads this tool
systematically times mdrun with various numbers of PME-only nodes and
determines which setting is fastest. It also checks whether performance can
be enhanced by shifting load between the real and the reciprocal space part
of the Ewald sum.
- g_membed: a very convenient utility for embedding membrane proteins
into equilibrated lipid bilayers


 Big thanks to all developers, contributors and users!

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Re: [gmx-users] Restarting after NVT: continuation error

2010-05-25 Thread Amit Choubey

On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI 
kumar...@buckeyemail.osu.edu wrote:


 Hello Gromacs Users,

 I am trying to make tpr file for NPT equilibration after NVT equilibration
 using

 grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o
 npt.tpr


 I am using  parameter  continuation = yes  in npt.mdp  for restarting
 after NVT, but I am getting this warning massage:


  WARNING 1 [file npt.mdp, line unknown]:
   Unknown left-hand 'continuation' in parameter file


well to continue why dont you use the same velocities ; just say gen_vel =
no

amit

 Please help me with this issue.

 Thank you
 --
 Vandana







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Re: [gmx-users] reading velocity in the g_msd routine

2010-05-18 Thread Amit Choubey

On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel gauravgoel...@gmail.comwrote:

 Hello gmx-users users :)

 I am modifying the 'g_msd' utility to be able to calculate viscosities
 using the corresponding Einstein relationship according to equation
 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is
 similar to the mean-square displacement equation for self-diffusion
 coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy'
 where p_iy is the particle momenta in y-direction.

 So basically I need to be able to read both position and velocities
 from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and
 'read_next_x' to read the coordinates. Can you please comment on how I
 can modify this code to read the corresponding velocities?


You could write your own little code to do that, see below for reading gro
format

http://manual.gromacs.org/current/online/gro.html

amit


 Any help is greatly appreciated.

 thanks,
 Gaurav
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Re: [gmx-users] pressure for ambient water

2010-05-17 Thread Amit Choubey

On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:



 On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:



On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Amit Choubey wrote:

   Hi Justin,

   Since the density (1 gm/cc) and T (300 K) correspond to
ambient
   condition, should not the equation of state dictate a
pressure
   around 1 atm?


   If the equation of state involves temperature and pressure, yes.

So if you fix the density and temperature shouldnt you land up
with right pressure which we know should be 1 atm.


You are not fixing (or conserving) the temperature in an NVE
ensemble.  That would be an NVT ensemble, employing a thermostat.

 I did do NVT first and then for sampling i removed the thermostat. Also as
 you mentioned there was not much difference b/n pressure values during NVT
 or NVE . The pressure value is as high as 1000 bar in both cases.


Since instantaneous pressure is calculated (in part) from the
kinetic energy, and since the kinetic energy is not guaranteed to be
conserved, the pressure term will also fluctuate accordingly.


 This is correct. The pressure thus fluctuates about 20 % of the above
 mentioned value.


http://www.gromacs.org/Documentation/Terminology/Pressure

The internal energy of the system is constant in an NVE ensemble,
the other terms may fluctuate as necessary such that all microstates
occur with the same probability and the energy surface remains flat.

 I agree

 Also recall that an NVE ensemble represents a thermodynamically
isolated system, not conducting heat or engaging in work with the
surrounding system.

 true

 So any concept of external pressure and equilibrating the pressure
is irrelevant.


 I am not trying to equilibriate the pressure. I am trying to measure the
 pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar.

 Also, theoretically NVE or NVT are no different than NPT as far as
 measuring observables is concerned. Hence i was thinking that if you have
 the right volume density and temperature shouldnt you have the right
 pressure.


 I think the disconnect is arising because you're expecting a model of water
 to behave almost like an ideal gas.  The SPC water model, under NPT
 conditions of 300 K and 1 bar, does not give the experimental density of
 water; it is actually somewhat less than 1 g/mL.  So constraining the system
 to fit some pre-conceived notion of the volume to force the density to be
 right conflicts with the properties of the water model itself.  SPC wants to
 be at a lower density, you're forcing it to be at a higher density, all
 while fixing the volume of the simulation cell.  Sounds to me like a recipe
 for high pressure, since SPC wants to expand but you won't let it.

 So the starting configuration, assembled with the right density, has not
 properly equilibrated under NPT conditions, yet you are expecting it to do
 so when applying NVE conditions.  I don't know that you'll ever be able to
 satisfy all of these requirements simultaneously unless you can come up with
 a better water model that replicates both ideal and real behavior :)


yes model is an issue too. I was just concerned about 3 orders of magnitude
of difference in calculation of pressure. Thank you for the answering.

amit


 -Justin


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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[gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey

Hi Everyone,

I was doing MD with SPC waters and found something which i am not sure how
to explain.

I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water
using grenbox .

I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling
and Reaction - Field for coulomb interaction. Cut off were all set to 1
nm. Temperature did converge to 300 K. After this i turned of nvt and did
nve with RF-zero for another ns. Energy was well converged during this (RMSD
 0.1 %). Temperature was also around 304 K (RMSD  1%). But the pressure
was 1.1 Kilobar with a fluctuation of 20 % . I don understand this, shouldnt
this be around 1 bar ? Could some one suggest whats on ?

Thank you,
amit
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Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey

Hi Justin,

Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
should not the equation of state dictate a pressure around 1 atm?

thank you
amit

On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi Everyone,

 I was doing MD with SPC waters and found something which i am not sure how
 to explain.

 I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water
 using grenbox .

 I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling
 and Reaction - Field for coulomb interaction. Cut off were all set to 1 nm.
 Temperature did converge to 300 K. After this i turned of nvt and did nve
 with RF-zero for another ns. Energy was well converged during this (RMSD 
 0.1 %). Temperature was also around 304 K (RMSD  1%). But the pressure was
 1.1 Kilobar with a fluctuation of 20 % . I don understand this, shouldnt
 this be around 1 bar ? Could some one suggest whats on ?


 Since an NVE ensemble employs neither a thermostat nor a barostat, I don't
 know why you'd expect that.

 -Justin

  Thank you,
 amit


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey

On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi Justin,

 Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
 should not the equation of state dictate a pressure around 1 atm?


 If the equation of state involves temperature and pressure, yes.


So if you fix the density and temperature shouldnt you land up with right
pressure which we know should be 1 atm.

amit



  thank you
 amit


 On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:

Hi Everyone,

I was doing MD with SPC waters and found something which i am
not sure how to explain.

I made a box of SPC water of dimension 4x4x4 nm^3 and filled
with water using grenbox .

I then did a nvt simulation at 300 K for 1 ns . I used berendsen
coupling and Reaction - Field for coulomb interaction. Cut off
were all set to 1 nm. Temperature did converge to 300 K. After
this i turned of nvt and did nve with RF-zero for another ns.
Energy was well converged during this (RMSD  0.1 %).
Temperature was also around 304 K (RMSD  1%). But the pressure
was 1.1 Kilobar with a fluctuation of 20 % . I don understand
this, shouldnt this be around 1 bar ? Could some one suggest
whats on ?


Since an NVE ensemble employs neither a thermostat nor a barostat, I
don't know why you'd expect that.

-Justin

Thank you,
amit


-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey

On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:



 On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:

Hi Justin,

Since the density (1 gm/cc) and T (300 K) correspond to ambient
condition, should not the equation of state dictate a pressure
around 1 atm?


If the equation of state involves temperature and pressure, yes.

 So if you fix the density and temperature shouldnt you land up with right
 pressure which we know should be 1 atm.



 You are not fixing (or conserving) the temperature in an NVE ensemble.
  That would be an NVT ensemble, employing a thermostat.


I did do NVT first and then for sampling i removed the thermostat. Also as
you mentioned there was not much difference b/n pressure values during NVT
or NVE . The pressure value is as high as 1000 bar in both cases.



 Since instantaneous pressure is calculated (in part) from the kinetic
 energy, and since the kinetic energy is not guaranteed to be conserved, the
 pressure term will also fluctuate accordingly.


This is correct. The pressure thus fluctuates about 20 % of the above
mentioned value.


 http://www.gromacs.org/Documentation/Terminology/Pressure

 The internal energy of the system is constant in an NVE ensemble, the other
 terms may fluctuate as necessary such that all microstates occur with the
 same probability and the energy surface remains flat.


I agree


  Also recall that an NVE ensemble represents a thermodynamically isolated
 system, not conducting heat or engaging in work with the surrounding system.



true


  So any concept of external pressure and equilibrating the pressure is
 irrelevant.


I am not trying to equilibriate the pressure. I am trying to measure the
pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar.

Also, theoretically NVE or NVT are no different than NPT as far as measuring
observables is concerned. Hence i was thinking that if you have the right
volume density and temperature shouldnt you have the right pressure.


 -Justin

  amit



thank you
amit


On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Amit Choubey wrote:

   Hi Everyone,

   I was doing MD with SPC waters and found something which i
 am
   not sure how to explain.

   I made a box of SPC water of dimension 4x4x4 nm^3 and filled
   with water using grenbox .

   I then did a nvt simulation at 300 K for 1 ns . I used
berendsen
   coupling and Reaction - Field for coulomb interaction.
Cut off
   were all set to 1 nm. Temperature did converge to 300 K.
After
   this i turned of nvt and did nve with RF-zero for another
 ns.
   Energy was well converged during this (RMSD  0.1 %).
   Temperature was also around 304 K (RMSD  1%). But the
pressure
   was 1.1 Kilobar with a fluctuation of 20 % . I don
 understand
   this, shouldnt this be around 1 bar ? Could some one suggest
   whats on ?


   Since an NVE ensemble employs neither a thermostat nor a
barostat, I
   don't know why you'd expect that.

   -Justin

   Thank you,
   amit


   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540)

231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
   -- gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org
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-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http

Re: [gmx-users] How to merge 2 simulation boxes?

2010-03-26 Thread Amit Choubey

On Thu, Mar 25, 2010 at 9:49 PM, 程迪 chengdi123...@gmail.com wrote:

 Hi, everyone

 I have two simulations which could run well separately. Now I want to place
 the box of simulation A onto the box of simulation B. What should I do to
 realise that?

 I've tried to copy and paste the .gro and .top file together, but there are
 several mistakes in grompp. I wonder if there are some better method to
 merge 2 simulation boxes.


copying straight forward will not help, you have to move the atoms of one of
the box by the box vectors of the other box. Does this make sense ?



 Di Cheng

 University of Science and Technology of China
 Hefei, Anhui Province 230026
 P. R. China
 E-mail: chen...@mail.ustc.edu.cn
 Tel.: +86-15321055911


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Re: [gmx-users] diffusion coefficient of oxygen molecule

2010-03-05 Thread Amit Choubey

Hi,

If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper

http://pubs.acs.org/doi/abs/10.1021/jp003020w

Also P,T coupling have effects on Diffusion Coeff.


amit

On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa mephy...@yahoo.com wrote:

 Respected experts
 I want to calculate the self diffusion cofficient of an oxygen molecule in
 water. The experimental value in the literature is found to be 2.5 x 10-9
 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off
 Lennard Jones interaction between water and oxygen. I want to reproduce this
 value. In your experience, which model of water would give the closer value.
 I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units
 and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding
 potential has been taken to be harmonic. Any knowledge of related literature
 would be helpful because I could not find by googling.

 Your idea will really help me.
 Neal


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Re: [gmx-users] gromacs memory usage

2010-03-04 Thread Amit Choubey

Hi Mark and Alexey,

Thank you for taking the time to write the responses. Following is the info
about the cluster

[chou...@hpc-login2 ~]$ uname -a
Linux hpc-login2 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

[chou...@hpc2000 ~]$ mpiexec --version
Version 0.82, configure options: '--host=x86_64-redhat-linux-gnu'
'--build=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux'
'--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin'
'--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share'
'--includedir=/usr/include' '--libdir=/usr/lib64'
'--libexecdir=/usr/libexec' '--localstatedir=/var'
'--sharedstatedir=/usr/com' '--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--with-pbs=/usr/lib64/torque'
'--disable-p4-shmem' 'CFLAGS=-O2 -g' 'build_alias=x86_64-redhat-linux-gnu'
'host_alias=x86_64-redhat-linux-gnu' 'target_alias=x86_64-redhat-linux'

[chou...@hpc2000 ~]$ ifort --version
ifort (IFORT) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[chou...@hpc2000 ~]$ icc --version
icc (ICC) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.


Thanks for all the help.

Amit





2010/3/3 Alexey Shvetsov alexx...@gmail.com

 Hi

 Looks like your system simply runs out of memory. So power cycling nodes
 isnt
 needed. If your cluster runs linux then it already has OOM Killer that will
 kill processes that runs out of memory. Also having swap on nodes is a good
 idea even with huge amount  of memory.
 Memory usage for mpi processes will strongly depend on mpi implentation
 because some of them are usualy caching slave process memory (like usualy
 do
 mvapich2)

 So can you provide info about youre cluster setup.
 OS version (including kernel version)  uname -a
 mpi version  mpirun --version or mpiexec --version
 also compiler version that was used for compiling gromacs

 On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote:
  Hi Roland,
 
  I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
  about 154 M particles. This should be feasible according to the numbers.
  Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core
 then
 
  Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
  All other nodes 8*1.06 ~ 8.5 GB
 
  I am planning to try the same run on 64 nodes with 8 cores each again but
  not until i am a little more confident. The problem is if gromacs crashes
  due to memory it makes the nodes to hang and people have to recycle the
  power supply.
 
 
  Thank you,
 
 --
 Best Regards,
 Alexey 'Alexxy' Shvetsov
 Petersburg Nuclear Physics Institute, Russia
 Department of Molecular and Radiation Biophysics
 Gentoo Team Ru
 Gentoo Linux Dev
 mailto:alexx...@gmail.com
 mailto:ale...@gentoo.org
 mailto:ale...@omrb.pnpi.spb.ru

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Re: [gmx-users] gromacs memory usage

2010-03-03 Thread Amit Choubey

Hi Roland,

It says

gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version
1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for
GNU/Linux 2.6.9, not stripped

On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote:

 Amit,

 try the full line (with the file)

 Roland

 On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi Roland

 I tried 'which mdrun' but it only gives the path name of installation. Is
 there any other way to know if the installation is 64 bit ot not?

 Thank you,
 Amit


 On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote:

 Hi,

 do:
 file `which mdrun`
 and it should give:
 /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
 dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped

 If it is not 64 you need to compile with 64 and have a 64bit kernel.
 Since you asked before about 2GB large files this might indeed be your
 problem.

 Roland

 On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote:

 Hi Tsjerk,

 I tried to do a test run based on the presentation. But there was a
 memory related error (I had given a leverage of more than 2 GB).

 I did not understand the 64 bit issue, could you let me know wheres the
 documentation? I need to look into that.

 Thank you,
 amit


 On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Amit,

 I think the presentation gives right what you want: a rough estimate.
 Now as Berk pointed out, to allocate more than 2GB of memory, you need
 to compile in 64bit. Then, if you want to have a real feel for the
 memory usage, there's no other way than trying. But fortunately, the
 memory requirements of a (very) long simulation are equal to that of a
 very short one, so it doesn't need to cost much time.

 Cheers,

 Tsjerk

 On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com
 wrote:
  Hi Mark,
 
  Yes thats one way to go about it. But it would have been great if i
 could
  get a rough estimation.
 
  Thank you.
 
  amit
 
 
  On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham 
 mark.abra...@anu.edu.au
  wrote:
 
  On 3/03/2010 12:53 PM, Amit Choubey wrote:
 
 Hi Mark,
 
 I quoted the memory usage requirements from a presentation by
 Berk
 Hess, Following is the link to it
 
 
 
 
 http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
 
 l. In that presentation on pg 27,28 Berk does talk about memory
 usage but then I am not sure if he referred to any other
 specific
  thing.
 
 My system only contains SPC water. I want Berendsen T coupling
 and
 Coulomb interaction with Reaction Field.
 
 I just want a rough estimate of how big of a system of water can
 be
 simulated on our super computers.
 
  Try increasingly large systems until it runs out of memory. There's
 your
  answer.
 
  Mark
 
  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham 
 mark.abra...@anu.edu.au
  mailto:mark.abra...@anu.edu.au wrote:
 
 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com mailto:
 kgp.a...@gmail.com
 Date: Saturday, February 27, 2010 10:17
 Subject: Re: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 
   Hi Mark,
   We have few nodes with 64 GB memory and many other with 16 GB
 of
 memory. I am attempting a simulation of around 100 M atoms.
 
 Well, try some smaller systems and work upwards to see if you
 have a
 limit in practice. 50K atoms can be run in less than 32GB over
 64
 processors. You didn't say whether your simulation system can
 run on
 1 processor... if it does, then you can be sure the problem
 really
 is related to parallelism.
 
   I did find some document which says one need (50bytes)*NATOMS
 on
 master node, also one needs
(100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
 nodes. Is this true?
 
 In general, no. It will vary with the simulation algorithm
 you're
 using. Quoting such without attributing the source or describing
 the
 context is next to useless. You also dropped a parenthesis.
 
 Mark
 --
 gmx-users mailing list gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/searchbefore
 posting!
 Please don't post (un)subscribe requests to the list. Use the
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 mailto:gmx-users-requ...@gromacs.org.
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Re: [gmx-users] gromacs memory usage

2010-03-03 Thread Amit Choubey

Hi Roland,

I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
about 154 M particles. This should be feasible according to the numbers.
Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then

Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
All other nodes 8*1.06 ~ 8.5 GB

I am planning to try the same run on 64 nodes with 8 cores each again but
not until i am a little more confident. The problem is if gromacs crashes
due to memory it makes the nodes to hang and people have to recycle the
power supply.


Thank you,

amit

On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz rol...@utk.edu wrote:

 Hi,

 ok then it is compiled in 64bit.

 You didn't say how many cores each node has and on how many nodes you want
 to run.

 Roland


 On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi Roland,

 It says

 gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64,
 version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared
 libs), for GNU/Linux 2.6.9, not stripped


 On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote:

 Amit,

 try the full line (with the file)

 Roland

 On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi Roland

 I tried 'which mdrun' but it only gives the path name of installation.
 Is there any other way to know if the installation is 64 bit ot not?

 Thank you,
 Amit


 On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote:

 Hi,

 do:
 file `which mdrun`
 and it should give:
 /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
 dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped

 If it is not 64 you need to compile with 64 and have a 64bit kernel.
 Since you asked before about 2GB large files this might indeed be your
 problem.

 Roland

 On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote:

 Hi Tsjerk,

 I tried to do a test run based on the presentation. But there was a
 memory related error (I had given a leverage of more than 2 GB).

 I did not understand the 64 bit issue, could you let me know wheres
 the documentation? I need to look into that.

 Thank you,
 amit


 On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar 
 tsje...@gmail.comwrote:

 Hi Amit,

 I think the presentation gives right what you want: a rough estimate.
 Now as Berk pointed out, to allocate more than 2GB of memory, you
 need
 to compile in 64bit. Then, if you want to have a real feel for the
 memory usage, there's no other way than trying. But fortunately, the
 memory requirements of a (very) long simulation are equal to that of
 a
 very short one, so it doesn't need to cost much time.

 Cheers,

 Tsjerk

 On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com
 wrote:
  Hi Mark,
 
  Yes thats one way to go about it. But it would have been great if i
 could
  get a rough estimation.
 
  Thank you.
 
  amit
 
 
  On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham 
 mark.abra...@anu.edu.au
  wrote:
 
  On 3/03/2010 12:53 PM, Amit Choubey wrote:
 
 Hi Mark,
 
 I quoted the memory usage requirements from a presentation by
 Berk
 Hess, Following is the link to it
 
 
 
 
 http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
 
 l. In that presentation on pg 27,28 Berk does talk about
 memory
 usage but then I am not sure if he referred to any other
 specific
  thing.
 
 My system only contains SPC water. I want Berendsen T coupling
 and
 Coulomb interaction with Reaction Field.
 
 I just want a rough estimate of how big of a system of water
 can be
 simulated on our super computers.
 
  Try increasingly large systems until it runs out of memory.
 There's your
  answer.
 
  Mark
 
  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham 
 mark.abra...@anu.edu.au
  mailto:mark.abra...@anu.edu.au wrote:
 
 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com mailto:
 kgp.a...@gmail.com
 Date: Saturday, February 27, 2010 10:17
 Subject: Re: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 
   Hi Mark,
   We have few nodes with 64 GB memory and many other with 16
 GB of
 memory. I am attempting a simulation of around 100 M atoms.
 
 Well, try some smaller systems and work upwards to see if you
 have a
 limit in practice. 50K atoms can be run in less than 32GB over
 64
 processors. You didn't say whether your simulation system can
 run on
 1 processor... if it does, then you can be sure the problem
 really
 is related to parallelism.
 
   I did find some document which says one need
 (50bytes)*NATOMS on
 master node, also one needs
(100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for
 compute
 nodes. Is this true?
 
 In general, no. It will vary with the simulation algorithm
 you're

Re: [gmx-users] gromacs memory usage

2010-03-02 Thread Amit Choubey


 Hi Mark,

 I quoted the memory usage requirements from a presentation by Berk Hess,
 Following is the link to it


http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf


 l. In that presentation on pg 27,28 Berk does talk about memory usage but
 then I am not sure if he referred to any other specific thing.

 My system only contains SPC water. I want Berendsen T coupling and Coulomb
 interaction with Reaction Field.

 I just want a rough estimate of how big of a system of water can be
 simulated on our super computers.

 Thank you,

 Amit


On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com
 Date: Saturday, February 27, 2010 10:17
 Subject: Re: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  Hi Mark,
  We have few nodes with 64 GB memory and many other with 16 GB of memory.
 I am attempting a simulation of around 100 M atoms.

 Well, try some smaller systems and work upwards to see if you have a limit
 in practice. 50K atoms can be run in less than 32GB over 64 processors. You
 didn't say whether your simulation system can run on 1 processor... if it
 does, then you can be sure the problem really is related to parallelism.

  I did find some document which says one need (50bytes)*NATOMS on master
 node, also one needs
   (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is
 this true?

 In general, no. It will vary with the simulation algorithm you're using.
 Quoting such without attributing the source or describing the context is
 next to useless. You also dropped a parenthesis.

 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/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.
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Re: [gmx-users] gromacs memory usage

2010-03-02 Thread Amit Choubey

Hi Mark,

Yes thats one way to go about it. But it would have been great if i could
get a rough estimation.

Thank you.

amit


On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 3/03/2010 12:53 PM, Amit Choubey wrote:

Hi Mark,

I quoted the memory usage requirements from a presentation by Berk
Hess, Following is the link to it



 http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf

l. In that presentation on pg 27,28 Berk does talk about memory
usage but then I am not sure if he referred to any other specific
 thing.

My system only contains SPC water. I want Berendsen T coupling and
Coulomb interaction with Reaction Field.

I just want a rough estimate of how big of a system of water can be
simulated on our super computers.


 Try increasingly large systems until it runs out of memory. There's your
 answer.

 Mark

  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au
 mailto:mark.abra...@anu.edu.au wrote:

- Original Message -
From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org

  Hi Mark,
  We have few nodes with 64 GB memory and many other with 16 GB of
memory. I am attempting a simulation of around 100 M atoms.

Well, try some smaller systems and work upwards to see if you have a
limit in practice. 50K atoms can be run in less than 32GB over 64
processors. You didn't say whether your simulation system can run on
1 processor... if it does, then you can be sure the problem really
is related to parallelism.

  I did find some document which says one need (50bytes)*NATOMS on
master node, also one needs
   (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
nodes. Is this true?

In general, no. It will vary with the simulation algorithm you're
using. Quoting such without attributing the source or describing the
context is next to useless. You also dropped a parenthesis.

Mark
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org

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Please search the archive at http://www.gromacs.org/search before
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Re: [gmx-users] gromacs memory usage

2010-03-02 Thread Amit Choubey

Hi Tsjerk,

I tried to do a test run based on the presentation. But there was a memory
related error (I had given a leverage of more than 2 GB).

I did not understand the 64 bit issue, could you let me know wheres the
documentation? I need to look into that.

Thank you,
amit

On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Amit,

 I think the presentation gives right what you want: a rough estimate.
 Now as Berk pointed out, to allocate more than 2GB of memory, you need
 to compile in 64bit. Then, if you want to have a real feel for the
 memory usage, there's no other way than trying. But fortunately, the
 memory requirements of a (very) long simulation are equal to that of a
 very short one, so it doesn't need to cost much time.

 Cheers,

 Tsjerk

 On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote:
  Hi Mark,
 
  Yes thats one way to go about it. But it would have been great if i could
  get a rough estimation.
 
  Thank you.
 
  amit
 
 
  On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au
  wrote:
 
  On 3/03/2010 12:53 PM, Amit Choubey wrote:
 
 Hi Mark,
 
 I quoted the memory usage requirements from a presentation by Berk
 Hess, Following is the link to it
 
 
 
 
 http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
 
 l. In that presentation on pg 27,28 Berk does talk about memory
 usage but then I am not sure if he referred to any other specific
  thing.
 
 My system only contains SPC water. I want Berendsen T coupling and
 Coulomb interaction with Reaction Field.
 
 I just want a rough estimate of how big of a system of water can be
 simulated on our super computers.
 
  Try increasingly large systems until it runs out of memory. There's your
  answer.
 
  Mark
 
  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au
  mailto:mark.abra...@anu.edu.au wrote:
 
 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com
 Date: Saturday, February 27, 2010 10:17
 Subject: Re: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 
   Hi Mark,
   We have few nodes with 64 GB memory and many other with 16 GB of
 memory. I am attempting a simulation of around 100 M atoms.
 
 Well, try some smaller systems and work upwards to see if you have a
 limit in practice. 50K atoms can be run in less than 32GB over 64
 processors. You didn't say whether your simulation system can run on
 1 processor... if it does, then you can be sure the problem really
 is related to parallelism.
 
   I did find some document which says one need (50bytes)*NATOMS on
 master node, also one needs
(100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
 nodes. Is this true?
 
 In general, no. It will vary with the simulation algorithm you're
 using. Quoting such without attributing the source or describing the
 context is next to useless. You also dropped a parenthesis.
 
 Mark
 --
 gmx-users mailing list gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/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
 mailto:gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at http://www.gromacs.org/search before
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  interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 
 
  --
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 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist
 --
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Re: [gmx-users] gromacs memory usage

2010-03-02 Thread Amit Choubey

Hi Roland

I tried 'which mdrun' but it only gives the path name of installation. Is
there any other way to know if the installation is 64 bit ot not?

Thank you,
Amit

On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote:

 Hi,

 do:
 file `which mdrun`
 and it should give:
 /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
 dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped

 If it is not 64 you need to compile with 64 and have a 64bit kernel. Since
 you asked before about 2GB large files this might indeed be your problem.

 Roland

 On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi Tsjerk,

 I tried to do a test run based on the presentation. But there was a memory
 related error (I had given a leverage of more than 2 GB).

 I did not understand the 64 bit issue, could you let me know wheres the
 documentation? I need to look into that.

 Thank you,
 amit


 On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Amit,

 I think the presentation gives right what you want: a rough estimate.
 Now as Berk pointed out, to allocate more than 2GB of memory, you need
 to compile in 64bit. Then, if you want to have a real feel for the
 memory usage, there's no other way than trying. But fortunately, the
 memory requirements of a (very) long simulation are equal to that of a
 very short one, so it doesn't need to cost much time.

 Cheers,

 Tsjerk

 On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote:
  Hi Mark,
 
  Yes thats one way to go about it. But it would have been great if i
 could
  get a rough estimation.
 
  Thank you.
 
  amit
 
 
  On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au
  wrote:
 
  On 3/03/2010 12:53 PM, Amit Choubey wrote:
 
 Hi Mark,
 
 I quoted the memory usage requirements from a presentation by Berk
 Hess, Following is the link to it
 
 
 
 
 http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
 
 l. In that presentation on pg 27,28 Berk does talk about memory
 usage but then I am not sure if he referred to any other specific
  thing.
 
 My system only contains SPC water. I want Berendsen T coupling and
 Coulomb interaction with Reaction Field.
 
 I just want a rough estimate of how big of a system of water can
 be
 simulated on our super computers.
 
  Try increasingly large systems until it runs out of memory. There's
 your
  answer.
 
  Mark
 
  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham 
 mark.abra...@anu.edu.au
  mailto:mark.abra...@anu.edu.au wrote:
 
 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com
 
 Date: Saturday, February 27, 2010 10:17
 Subject: Re: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 
   Hi Mark,
   We have few nodes with 64 GB memory and many other with 16 GB
 of
 memory. I am attempting a simulation of around 100 M atoms.
 
 Well, try some smaller systems and work upwards to see if you have
 a
 limit in practice. 50K atoms can be run in less than 32GB over 64
 processors. You didn't say whether your simulation system can run
 on
 1 processor... if it does, then you can be sure the problem really
 is related to parallelism.
 
   I did find some document which says one need (50bytes)*NATOMS
 on
 master node, also one needs
(100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
 nodes. Is this true?
 
 In general, no. It will vary with the simulation algorithm you're
 using. Quoting such without attributing the source or describing
 the
 context is next to useless. You also dropped a parenthesis.
 
 Mark
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[gmx-users] gromacs memory usage

2010-02-26 Thread Amit Choubey

Hi,

I am having trouble with running gromacs with a large system. I am trying to
use several processors for the md. The error is a memory allocation error
and it might be due to low RAM or large no of particles. I want to know the
detailed memory usage of mdrun ie say for N atoms how much memory does the
master node need and then also whats the memory requirement for the other
nodes. By master node i mean the node that does the domain decomposition
calculation etc during the start of mdrun. A webpage which describes the
memory requirement at various stages during mdrun will be very helpful.

Thank you,
amit
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Re: [gmx-users] Choice of value of rlist, rvdw and rcoulomb

2010-02-26 Thread Amit Choubey

Hi Lum,

These values have to be chosen very icarefully.
Many artifacts can show up due to poorly chosen cutoff. I would suggest to
get the parameters from a reproducible publication or something.

amit

On Fri, Feb 26, 2010 at 8:49 AM, Lum Nforbi lumngwe...@gmail.com wrote:

 Hi all,

   Please, can someone let me know if the choice of the value of rlist, rvdw
 and rcoulomb is related to or depends in someway to the distance between
 atoms on a lennard-jones potential plot?

 I appreciate your answers.

 Lum

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Re: [gmx-users] gromacs memory usage

2010-02-26 Thread Amit Choubey

Hi Mark,

We have few nodes with 64 GB memory and many other with 16 GB of memory. I
am attempting a simulation of around 100 M atoms.

I did find some document which says one need (50bytes)*NATOMS on master
node, also one needs
 (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this
true?


Thank you,
amit

On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham mark.abra...@anu.edu.auwrote:)

 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com
 Date: Friday, February 26, 2010 20:05
 Subject: [gmx-users] gromacs memory usage
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  Hi,
  I am having trouble with running gromacs with a large system. I am trying
 to use several processors for the md. The error is a memory allocation error
 and it might be due to low RAM or large no of particles. I want to know the
 detailed memory usage of mdrun ie say for N atoms how much memory does the
 master node need and then also whats the memory requirement for the other
 nodes. By master node i mean the node that does the domain decomposition
 calculation etc during the start of mdrun. A webpage which describes the
 memory requirement at various stages during mdrun will be very helpful.

 The master node does not have a significantly larger memory footprint than
 any other, during setup or the run... For example, a 50K-atom system runs
 fine on 64 BlueGene/L processors with a hard limit of 500MB per processor
 for OS+code+data+MPI.

 Does your system run on 1 processor, with and without MPI? How much
 (physical) memory do you have for how large a system?

 Mark
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[gmx-users] water simulation

2010-02-23 Thread Amit Choubey

Hi everyone,

I am afraid this is not really a gromacs related question. Could anyone
refer me to a review paper which discusses about simulating water? Does any
of them gives a comparative and complete study of molecular dynamics with
water , answering questions like which water model to use, how to deal with
coulomb interaction, what should be the cutoff value (if cutoff is used) . I
have not been able to find one with complete story. Is anyone aware of such
a publication.

Thank you,
Amit
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[gmx-users] writing forces in gromacs

2010-02-22 Thread Amit Choubey

Hi everyone,

I had been trying to work with forces of the atoms and stumbled upon
something weird.

In my md.mdp file i ask to write forces with a certain frequency then the
grompp shows a seemingly harmless note, the full md.mdp and extract of the
grompp.out are as follows :-

title   =  Yo
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  8500 ; total 17 ps.
nstcomm =  0
nstxout =  500
nstvout =  500
*nstfout =   500*
nstlog  =  100
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.3
coulombtype=  Reaction-Field-zero
rcoulomb=  1.0
epsilon_rf=  0
vdwtype=  Shift
rvdw=  1.0
rvdw_switch=  0.9
Tcoupl  =  no
energygrps  =   DPPC SOL
Pcoupl  =  no
gen_vel =  no
lincs_iter=   2

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinations
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.dat
Making dummy/rest group for T-Coupling containing 1933647 elements
Making dummy/rest group for Acceleration containing 1933647 elements
Making dummy/rest group for Freeze containing 1933647 elements
Making dummy/rest group for VCM containing 1933647 elements
Number of degrees of freedom in T-Coupling group rest is 3924894.00
Making dummy/rest group for User1 containing 1933647 elements
Making dummy/rest group for User2 containing 1933647 elements
Making dummy/rest group for XTC containing 1933647 elements
Making dummy/rest group for Or. Res. Fit containing 1933647 elements
Making dummy/rest group for QMMM containing 1933647 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 2 element(s): DPPC SOL
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

*NOTE 1 [file nve.mdp, line unknown]:*
  This run will generate roughly 2493 Mb of data

writing run input file...

There was 1 note

gcq#197: I Do It All the Time (Magnapop)

 :-)  G  R  O  M  A  C  S  (-:



Now when i change nstfout to zero (no printing of forces) the note doesnt
show up anymore.

Also for the case with nstfout = 500 it seems that the forces are being read
and written properly, I tried the g_traj tool to see the forces.

Could someone clarify?

Thank you,
Amit Choubey
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[gmx-users] domain decomposition and load balancing

2010-02-19 Thread Amit Choubey

Hi Everyone,

I am trying to run a simulation with the option pbc=xy turned on. I am
using 64 processors for the simulation. The mdrun_mpi evokes the following
error message before starting the md steps

There is no domain decomposition for 64 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

This has to do with the load balancing in the domain decomposition version
of mdrun. Can anyone suggest me how to set the option -rdd or -dds?

Also the simulation runs fine on one node (with domain decomposition) and
with particle decomposition but both of them extremely slow.


Thank you,
Amit
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Re: [gmx-users] domain decomposition and load balancing

2010-02-19 Thread Amit Choubey

Hi Mark,

I am not using PME calculation.

I was hoping mdrun will do the cell allocation itself.

Thanks,
Amit


On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com
 Date: Saturday, February 20, 2010 8:51
 Subject: [gmx-users] domain decomposition and load balancing
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  Hi Everyone,
  I am trying to run a simulation with the option pbc=xy turned on. I am
 using 64 processors for the simulation. The mdrun_mpi evokes the following
 error message before starting the md steps
 
  There is no domain decomposition for 64 nodes that is compatible with the
 given box and a minimum cell size of 0.889862 nm Change the number of nodes
 or mdrun option -rdd or -dds
 Look in the log file for details on the domain decomposition
  This has to do with the load balancing in the domain decomposition
 version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?

 Those options are not normally the problem - but see the log file for info
 and mdrun -h for instructions.

 You should read up in the manual about domain decomposition, and see about
 choosing npme such that 64-npme is a number that is suitably composite that
 you can make a reasonably compact 3D grid so that the minimum cell size is
 not a constraint. Cells have to be large enough that all nonbonded
 interactions can be resolved in consultation with at most nearest-neighbour
 cells (and some other constraints).

 I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45
 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the
 cells to have the smallest diameter possible. Of course if your simulation
 box is so small that the 2D DD for pbc=xy will always lead to slabs that are
 too small in one dimension then you can't solve this problem with DD.

 If pbc=xy permits a 3D DD, then the same considerations apply. npme=19
 gives 5x3x3 but npme=28 allows 4x3x3

  Also the simulation runs fine on one node (with domain decomposition) and
 with particle decomposition but both of them extremely slow.

 Well, that's normal...

 Mark
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Re: [gmx-users] domain decomposition and load balancing

2010-02-19 Thread Amit Choubey

Hi Mark,

I dont think i need to play with npme at all.

Amit

On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey kgp.a...@gmail.com wrote:

 Hi Mark,

 I am not using PME calculation.

 I was hoping mdrun will do the cell allocation itself.

 Thanks,
 Amit


 On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com
 Date: Saturday, February 20, 2010 8:51
 Subject: [gmx-users] domain decomposition and load balancing
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  Hi Everyone,
  I am trying to run a simulation with the option pbc=xy turned on. I am
 using 64 processors for the simulation. The mdrun_mpi evokes the following
 error message before starting the md steps
 
  There is no domain decomposition for 64 nodes that is compatible with
 the given box and a minimum cell size of 0.889862 nm Change the number of
 nodes or mdrun option -rdd or -dds
 Look in the log file for details on the domain decomposition
  This has to do with the load balancing in the domain decomposition
 version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?

 Those options are not normally the problem - but see the log file for info
 and mdrun -h for instructions.

 You should read up in the manual about domain decomposition, and see about
 choosing npme such that 64-npme is a number that is suitably composite that
 you can make a reasonably compact 3D grid so that the minimum cell size is
 not a constraint. Cells have to be large enough that all nonbonded
 interactions can be resolved in consultation with at most nearest-neighbour
 cells (and some other constraints).

 I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45
 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the
 cells to have the smallest diameter possible. Of course if your simulation
 box is so small that the 2D DD for pbc=xy will always lead to slabs that are
 too small in one dimension then you can't solve this problem with DD.

 If pbc=xy permits a 3D DD, then the same considerations apply. npme=19
 gives 5x3x3 but npme=28 allows 4x3x3

  Also the simulation runs fine on one node (with domain decomposition)
 and with particle decomposition but both of them extremely slow.

 Well, that's normal...

 Mark
 --
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Re: [gmx-users] domain decomposition and load balancing

2010-02-19 Thread Amit Choubey

the log file just lists all the parameters of the simulation, following is a
part of it

parameters of the run:
   integrator   = md
   nsteps   = 4000
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 0
   comm_mode= Linear
   nstlog   = 1000
   nstxout  = 1000
   nstvout  = 0
   nstfout  = 500
   nstenergy= 10
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 0
   nky  = 0
   nkz  = 0
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xy
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1.3
   rtpi = 0.05
   coulombtype  = Reaction-Field-zero
   rcoulomb_switch  = 0
   rcoulomb = 1
   vdwtype  = Shift
   rvdw_switch  = 0.9
   rvdw = 1
   epsilon_r= 1
   epsilon_rf   = inf
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = No
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtype[0] = -1
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 10
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 2
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:  3.92594e+06
   ref_t:   0
   tau_t:   0
anneal:  No
ann_npoints:   0
   acc:   0   0   0
   nfreeze:   N   N   N
   energygrp_flags[  0]: 0 0
   energygrp_flags[  1]: 0 0
   efield-x:
  n = 0
   efield-xt:
  n = 0
   efield-y:
  n = 0
   efield-yt:
  n = 0
   efield-z:
  n = 0
   efield-zt:
  n = 0
   bQMMM= FALSE
   QMconstraints= 0
   QMMMscheme   = 0
   scalefactor  = 1
qm_opts:
   ngQM = 0


On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote:



 - Original Message -
 From: Amit Choubey kgp.a...@gmail.com
 Date: Saturday, February 20, 2010 10:25
 Subject: Re: [gmx-users] domain decomposition and load balancing
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  Hi Mark and Justin,
  I am using a box of size (20nm)x(20nm)x(60nm

[gmx-users] pbc option

2010-02-15 Thread Amit Choubey

Hi Everyone,

I changed the gromacs source code a little bit and this change introduced
some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the
option of pbc = xy only. Is there a quick tip to circumvent? I can always
introduce the bias along z but its a little time taking job :)

Amit
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[gmx-users] diffusion coefficient

2010-02-10 Thread Amit Choubey

Hi Everyone,

I have been trying to calculate diffusion coefficient for water. I am trying
to reproduce the numbers published in journal papers.
I am using SPCE water model. I use the g_msd analysis tool.

g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8

I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I
equilibriate the system for a ns and then run for additional 10 ps for
analysis. Here are some of the numbers that i get

a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/-
0.2992) 1e-5 cm^2/s
b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/-
0.1076) 1e-5 cm^2/s
c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P
coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s
.

c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s
but its not quite right.

Could someone explain to me why the values obtained in above 3 cases are
widely different and may be give some tips about the right procedure to
calculate diffusion (method and invoking the g_msd tool)?

Thank you
Amit
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Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey

Hi Mark,

That is true. But what does the manual refer to when it says

the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there might be a
hidden feature that could be useful for me.

Amit

On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

 Amit Choubey wrote:

 Hi Mark,

 Ok here is the command line i used :-

 g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
 output is
 # This file was created Tue Dec  1 20:20:41 2009
 # by the following command:
 # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
 #
 # g_angle is part of G R O M A C S:
 #
 # Go Rough, Oppose Many Angry Chinese Serial killers
 #
 @title Dihedral Distribution: C34_C36_C37_C38


 This title makes it look like there is only one angle in your index file.

 Mark

  @xaxis  label Degrees
 @yaxis  label 
 @TYPE xy
 @subtitle average angle: 9.87432\So\N
 @with g0
 @world xmin -180
 @world xmax  180
 @world ymin 0
 @world ymax 0.0451172
 @xaxis  tick major 60
 @xaxis  tick minor 30
 @yaxis  tick major 0.005
 @yaxis  tick minor 0.0025
  -1800.015625
  -1790.011719
  -1780.015625
  -1770.00
  -1760.035156
  -1750.031250
  -1740.019531
  -1730.019531
  -1720.023438
  -1710.015625
  -1700.015625

 I did not include the distribution for rest of the angles.
  The second column is the fractional distribution of dihedrals with the
 corresponding angle in the 1st column.

 The distribution is averaged over time t = 800ps and 802 ps snapshots. I
 checked this part.

 Amit




 On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham mark.abra...@anu.edu.aumailto:
 mark.abra...@anu.edu.au wrote:

Amit Choubey wrote:

Hi Mark,

It does seem that the -all option averages the distributions.
The thing is i was confused with the first graph is the
average, the rest are the individual angles. because when i
tried it previously i only found 2 columns which were angle and
distribution.

But now i checked again explicitly by doing few more g_angle
commands and it seems that -all does do what i wanted to do. I
still dont know what the rest are the individual angles means.


I haven't ever used it, but would have expected the output to be
along the lines of

Time Average over all angles Angle-1 Angle-2 ...
1  234   23  345
2  123   234 232
2  223   ...
3  323

What output do you get and what seems wrong to you?

Mark

On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:

   Amit Choubey wrote:

   Hi everyone,

   I am trying to analyze dihedrals of molecules after a
   simulation. I am able to calculate dihedral distribution
at ant
   particular time using g
   -angle and proper group using

   g_angle -f after_md.trr -b 800 -type dihedral -n
chain1.ndx -od
   dihed12

   This gives me the distribution at t=800 ps . What i
really want
   is to see the dihedral distribution at all time steps
(after 800
   ps) in one go, and may be do some averaging later. Is there
 a
   straight forward way to do this. I can imagine that i could
   write a script file that could do this but then i dont
want to
   deal with a lot of files, i rather want everything to be
saved
   in a single file with multiple columns. Could someone
suggest a
   trick for this?


   The first paragraph of g_angle -h suggests there's an option
where
   the first graph is the average, the rest are the individual
   angles. Does this work?


   Mark
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mailto:gmx-users@gromacs.org
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Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey

On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:

 Hi Mark,

 That is true. But what does the manual refer to when it says
 the first graph is the average, the rest are the individual angles

 what and where are the rest? I am only curious because there might be a
 hidden feature that could be useful for me.


 Read all of the help information; the command in the .xvg file below shows
 that you're not yet using the right output options.  Hint: look at the
 sentence in g_angle -h before the one quoted above, as well as the -ov
 flag...


-ov flag gives the average value of angle of the group with time. This is
not very useful for me right now.

I am interested in the distribution of dihedrals with angle.

I was just curious about the -all features...




 -Justin

  Amit


 On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham 
 mark.abra...@anu.edu.aumailto:
 mark.abra...@anu.edu.au wrote:

Amit Choubey wrote:

Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
804 -all
output is
# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title Dihedral Distribution: C34_C36_C37_C38


This title makes it look like there is only one angle in your index
file.

Mark

@xaxis  label Degrees
@yaxis  label 
@TYPE xy
@subtitle average angle: 9.87432\So\N
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
 -1800.015625
 -1790.011719
 -1780.015625
 -1770.00
 -1760.035156
 -1750.031250
 -1740.019531
 -1730.019531
 -1720.023438
 -1710.015625
 -1700.015625

I did not include the distribution for rest of the angles.
 The second column is the fractional distribution of dihedrals
with the corresponding angle in the 1st column.

The distribution is averaged over time t = 800ps and 802 ps
snapshots. I checked this part.

Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:

   Amit Choubey wrote:

   Hi Mark,

   It does seem that the -all option averages the
 distributions.
   The thing is i was confused with the first graph is the
   average, the rest are the individual angles. because when i
   tried it previously i only found 2 columns which were
angle and
   distribution.

   But now i checked again explicitly by doing few more g_angle
   commands and it seems that -all does do what i wanted to
do. I
   still dont know what the rest are the individual angles
means.


   I haven't ever used it, but would have expected the output to be
   along the lines of

   Time Average over all angles Angle-1 Angle-2 ...
   1  234   23  345
   2  123   234 232
   2  223   ...
   3  323

   What output do you get and what seems wrong to you?

   Mark

   On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
   mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
   mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
   mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:

  Amit Choubey wrote:

  Hi everyone,

  I am trying to analyze dihedrals of molecules after a
  simulation. I am able to calculate dihedral
distribution
   at ant
  particular time using g
  -angle and proper group using

  g_angle -f after_md.trr -b 800 -type dihedral -n
   chain1.ndx -od
  dihed12

  This gives me the distribution at t=800 ps . What i
   really want
  is to see the dihedral distribution at all time

Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey

Hi Justin,

Yes I understand what you are saying.

Thank you

amit

On Wed, Dec 2, 2009 at 12:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Amit Choubey wrote:



 On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Amit Choubey wrote:

Hi Mark,

That is true. But what does the manual refer to when it says
the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there
might be a hidden feature that could be useful for me.


Read all of the help information; the command in the .xvg file below
shows that you're not yet using the right output options.  Hint:
look at the sentence in g_angle -h before the one quoted above, as
well as the -ov flag...


 -ov flag gives the average value of angle of the group with time. This is
 not very useful for me right now.


 By using -ov -all, the first column is the average of all groups analyzed,
 and probably is not useful for your purpose, but the subsequent columns are
 the value of the chosen angles at each time frame.  From these data, you
 could pretty easily write a script that calculates the distributions by
 binning.

 -Justin


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey

Hi everyone,

I am trying to analyze dihedrals of molecules after a simulation. I am able
to calculate dihedral distribution at ant particular time using g
-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12

This gives me the distribution at t=800 ps . What i really want is to see
the dihedral distribution at all time steps (after 800 ps) in one go, and
may be do some averaging later. Is there a straight forward way to do this.
I can imagine that i could write a script file that could do this but then i
dont want to deal with a lot of files, i rather want everything to be saved
in a single file with multiple columns. Could someone suggest a trick for
this?

Thank you,
Amit
-- 
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey

Hi Mark,

It does seem that the -all option averages the distributions.
The thing is i was confused with the first graph is the average, the rest
are the individual angles. because when i tried it previously i only found
2 columns which were angle and distribution.

But now i checked again explicitly by doing few more g_angle commands and it
seems that -all does do what i wanted to do. I still dont know what the
rest are the individual angles means.



Thank you,
Amit






On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 Amit Choubey wrote:

 Hi everyone,

 I am trying to analyze dihedrals of molecules after a simulation. I am
 able to calculate dihedral distribution at ant particular time using g
 -angle and proper group using

 g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12

 This gives me the distribution at t=800 ps . What i really want is to see
 the dihedral distribution at all time steps (after 800 ps) in one go, and
 may be do some averaging later. Is there a straight forward way to do this.
 I can imagine that i could write a script file that could do this but then i
 dont want to deal with a lot of files, i rather want everything to be saved
 in a single file with multiple columns. Could someone suggest a trick for
 this?


 The first paragraph of g_angle -h suggests there's an option where the
 first graph is the average, the rest are the individual angles. Does this
 work?


 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/search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey

Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all

output is

# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title Dihedral Distribution: C34_C36_C37_C38
@xaxis  label Degrees
@yaxis  label 
@TYPE xy
@subtitle average angle: 9.87432\So\N
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
  -1800.015625
  -1790.011719
  -1780.015625
  -1770.00
  -1760.035156
  -1750.031250
  -1740.019531
  -1730.019531
  -1720.023438
  -1710.015625
  -1700.015625

I did not include the distribution for rest of the angles.

The second column is the fractional distribution of dihedrals with the
corresponding angle in the 1st column.

The distribution is averaged over time t = 800ps and 802 ps snapshots. I
checked this part.

Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 Amit Choubey wrote:

 Hi Mark,

 It does seem that the -all option averages the distributions. The thing is
 i was confused with the first graph is the average, the rest are the
 individual angles. because when i tried it previously i only found 2
 columns which were angle and distribution.

 But now i checked again explicitly by doing few more g_angle commands and
 it seems that -all does do what i wanted to do. I still dont know what the
 rest are the individual angles means.


 I haven't ever used it, but would have expected the output to be along the
 lines of

 Time Average over all angles Angle-1 Angle-2 ...
 1  234   23  345
 2  123   234 232
 2  223   ...
 3  323

 What output do you get and what seems wrong to you?

 Mark

  On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.aumailto:
 mark.abra...@anu.edu.au wrote:

Amit Choubey wrote:

Hi everyone,

I am trying to analyze dihedrals of molecules after a
simulation. I am able to calculate dihedral distribution at ant
particular time using g
-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od
dihed12

This gives me the distribution at t=800 ps . What i really want
is to see the dihedral distribution at all time steps (after 800
ps) in one go, and may be do some averaging later. Is there a
straight forward way to do this. I can imagine that i could
write a script file that could do this but then i dont want to
deal with a lot of files, i rather want everything to be saved
in a single file with multiple columns. Could someone suggest a
trick for this?


The first paragraph of g_angle -h suggests there's an option where
the first graph is the average, the rest are the individual
angles. Does this work?


Mark
--gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
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[gmx-users] g_angle for calculating dihedrals

2009-11-28 Thread Amit Choubey

Hi everyone,

I was looking at calculation od dihedrals using g_angle. I did not
understand what the output of this tool is, along the x-axis we have angle
(in degrees) but what do we have along the y axis . Does y-axis show the
fraction of dihedrals having that specific angle? It does seem so by adding
all the fractions but i need to make sure.

Just to be sure that you know what i am talking about i first used make_ndx
to make a group of 4 atoms (whose dihedral has to be calculated) . Then i
used

g_angle -f confout.gro -n index.ndx -type dihedral

where index.ndx has the indices for all the relevant atoms stored in a
group.

Thank you,

Amit
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Re: [gmx-users] Problem with box-type after the extension of simulation

2009-11-18 Thread Amit Choubey

On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain suk...@atc.tcs.comwrote:

 Dear All,
 I started a protein simulation for 100ps with octahedron box. After
 completion of that run I visualized the protein at the centre of the
 octahedron box by using trjconv.
 Then I have extended the simulation for another 500 ps by using tpbconv.
 But now it is showing as cubic box when I see the result after using
 trajconv (additionally some part of the protein is out of the box).


This could only be a visualization glitch.
Try using trjconv options.

amit


 I do not have any clue how the box type has been changed or where could I
 go wrong.
 Please comment.
 Thank you,
 Cheers,
 Sukesh

 --
 Sukesh Chandra Gain
 TCS Innovation Labs
 Tata Consultancy Services Ltd.
 'Deccan Park', Madhapur
 Hyderabad 500081
 Phone:  +91 40 6667 3572

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Re: [gmx-users] Handling modified residue

2009-11-14 Thread Amit Choubey

you could try to write your top files in the working directory and use
pdb2gmx -ff option. By default, gromacs first searches in the working
directory.

amit

On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu zhujiang2...@gmail.com wrote:

 Dear all,

 I have been a GROMACS user for some time but this is my first time
 to handle a modified residue with an additional chemical group linked to the
 side chain. I do not have the permission to change/add the topology file in
 the system directory where GROMACS package is located. I am wondering if
 there is any other way to force pdbgmx to read residue topo file from
 specified location or other tricks I can play. Thanks for your help!

 Best regards,
 Jiang

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Re: [gmx-users] Segmentation fault while running MD simulation

2009-11-13 Thread Amit Choubey

hi,

could you specify the system size?

How many steps did it run before you got the segmentation fault? Try to find
if everything went ok until the segmentation fault by saving log and
trajectories.

amit



On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 rainy...@yahoo.com wrote:

 Hi,

 The relevant lines of my script are the following:

 line 27: # Run MD and write output to /nas2 disk
 line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
 confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
 line 29:
 line 30: # MDRUN completes: now make the next run file for a further 200
 ps, to be run by next job
 line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o
 npg3_4_2.tpr -extend 20


 Since line 31 would be carried out after line 28, I'm not sure why the
 comment -s: command not found is relevant?


 Because mdrun is exiting, so the script is moving on.  Perhaps the system
 isn't recognizing the $TPBCONV environment variable, and thus is
 interpreting -s as a separately command rather than an option passed to
 tpbconv.

 -Justin



 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] Can not open file; traj.trr

2009-11-13 Thread Amit Choubey

in your previous run you might be saving the trajectory in some other *.trr
file . Try appending in that.

amit

On Fri, Nov 13, 2009 at 9:11 AM, Yi Peng muhuohuo...@gmail.com wrote:

 Hi, everyone,

 I was using Gromacs-4.0.3 to run my MD calculations parallell on our High
 performance clusters for a large system which was crashed because I run out
 the time limits. So I tried to resume my calculations by the script as
 follows:

 #PBS -N gromacs
 #PBS -l walltime=250:00:00
 #PBS -l nodes=8:ppn=2:quad
 #PBS -j oe
 echo Using nodes
 cat $PBS_NODEFILE
 module load mpich
 module load intel-f
 module load gromacs-4.0.3
 cd $PBS_O_WORKDIR
 cd /home/yxp17/impd/impd1/wt_wo
 /usr/local/bin/mpiexec mdrun -multi 16 -s md.tpr -cpi state.cpt -append


 But it will stop and show the message as follows

 Whatever Happened to Pong ? (F. Black)
 Halting program mdrun
 gcq#180: Whatever Happened to Pong ? (F. Black)
 [0] MPI Abort by user Aborting program !
 [0] Aborting program!
 p0_12952:  p4_error: : -1
 p4_error: latest msg from perror: No such file or directory
 ---
 Program mdrun, VERSION 4.0.3
 Source code file: gmxfio.c, line: 736
 Can not open file:
 traj.trr
 ---
 How can I solve the problem? Thanks a lot

 Yi

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[gmx-users] Re: Walls In Gromacs

2009-11-10 Thread Amit Choubey

On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir amarcov...@gmail.comwrote:

 Hi Amit,

 Unfortunately, i don't have an answer to your question as i am a very
 new GROMACS user myself..
 Actually i might need your help.



 I need to model two charged plates with opposite signs which are
 solvated in an electrolyte solution.


You might try to start with a boundary condition on the potential say
something like constant potential on the plates. And then you can always
find the electrostatic Green's function that solves the poisson's equation.
From there you could derive an expression for the potential in the box if
the charge density were provided. This part is discussed in Classic
Electrodynamics book by Jackson. Have a look at it if you need reference.

You can use the above green's function for finding potential everywhere in
box depending on the location of ions in the solution. The force due to this
can then be implemented in MD. I am not very sure about the implementation
though.


 When I was desperately browsing for
 keywords such as: Gromacs plates, walls, etc., trying to find the
 slightest clue of how to approach this issue in gromacs i saw your
 posting from the October 19th.

 I will most appreciate if you can give me some hint or tip of how to
 approach this problem or what is the suitable chapter in the manual to
 search for it.


I am not sure about any discussion on the specific type of things you are
talking about. Wall function for MD simulation is disscussed in chapter 7.
You will only find what options can be used. I think a tabulated function
can also be used.


 Sorry i couldn't help you with your question, hopefully you already
 figured it out,



I think it beneficial for both of us to keep these discussion in the forum
for our and other's benefit .

Amit


 Regards,
 Amir Marcovitz,
 Weizmann Inst. of Science , Rehovot, Israel

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[gmx-users] doing exact continuation

2009-11-10 Thread Amit Choubey

Hi everyone,

I want to do an exact continuation with saved configuration and velocity.
What are the options that i need to change in mdp file?

I know i have to make unconstrained_start = yes. Anything else?

The reason i am asking this is that it is kind of difficult to make sure if
i am doing the right thing by comparing two different trajectories. This is
because the trajectories are generally 'chaotic' and they diverge even if
there is a difference in the numbers due to the machine. So i want to do the
best from my part.

thank you,
Amit
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Re: [gmx-users] How to generate xvg files

2009-11-10 Thread Amit Choubey

On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz 
j...@drugdiscoveryathome.comwrote:

 Hi I am trying to generate xvg files for my simulation. Which
 parameter do I need to specify?


xvg files for what? They are used for data files for 2D plots of quantities
that can be analyzed...

Can you be more specific?

amit


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Re: [gmx-users] How to generate xvg files

2009-11-10 Thread Amit Choubey

On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz 
j...@drugdiscoveryathome.comwrote:

 Actually I guess I need to generate the xtc first before I can get the xvg

 I am trying to develop a workflow for this
 mdrun
 g dist calculates the distances between the centers of mass of two groups
 g bond calculates distances between atoms
 g msd calculates mean square displacements
 g rms calculates rmsd’s with a reference structure and rmsd matrices
 g rmsf calculates atomic fluctuations
 g energy writes energies to xvg files and displays averages


Thats true. First you need to do the simulation 'mdrun' and then analyze the
trajectory (.xtc) and energy (.edr) files generated. It takes quite some
time to figure out the first step 'mdrun' :)

amit





 On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey kgp.a...@gmail.com wrote:
 
 
  On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz j...@drugdiscoveryathome.com
 
  wrote:
 
  Hi I am trying to generate xvg files for my simulation. Which
  parameter do I need to specify?
 
  xvg files for what? They are used for data files for 2D plots of
 quantities
  that can be analyzed...
  Can you be more specific?
  amit
 
  --
  Jack
 
  http://drugdiscoveryathome.com
  http://hydrogenathome.org
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Re: [gmx-users] How to generate xvg files

2009-11-10 Thread Amit Choubey

On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz 
j...@drugdiscoveryathome.comwrote:

 I'm trying to get the xtc output. The mdp file has these parameters.
 Is the nstxtcout what specifiies it to generate xtc?

yes its the freq of writing co - ordinates

 nsteps  = 2000  ; Maximum number of (minimization)
 steps to perform
 nstenergy   = 10; Write energies to disk every nstenergy
 steps
 nstxtcout   = 10; Write coordinates to disk every
 nstxtcout steps

 Do I need to use this -x flag?
 mdrun -nice 0 -s em.tpr -x
 No xtc was created though

-x is for writing xtc file
http://manual.gromacs.org/current/online/mdrun.html should help


 On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey kgp.a...@gmail.com wrote:
 
 
  On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz j...@drugdiscoveryathome.com
 
  wrote:
 
  Actually I guess I need to generate the xtc first before I can get the
 xvg
 
  I am trying to develop a workflow for this
  mdrun
  g dist calculates the distances between the centers of mass of two
 groups
  g bond calculates distances between atoms
  g msd calculates mean square displacements
  g rms calculates rmsd’s with a reference structure and rmsd matrices
  g rmsf calculates atomic fluctuations
  g energy writes energies to xvg files and displays averages
 
  Thats true. First you need to do the simulation 'mdrun' and then analyze
 the
  trajectory (.xtc) and energy (.edr) files generated. It takes quite some
  time to figure out the first step 'mdrun' :)
  amit
 
 
 
  On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey kgp.a...@gmail.com
 wrote:
  
  
   On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
   j...@drugdiscoveryathome.com
   wrote:
  
   Hi I am trying to generate xvg files for my simulation. Which
   parameter do I need to specify?
  
   xvg files for what? They are used for data files for 2D plots of
   quantities
   that can be analyzed...
   Can you be more specific?
   amit
  
   --
   Jack
  
   http://drugdiscoveryathome.com
   http://hydrogenathome.org
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  --
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