[gmx-users] About Compiler Compatibility for Gromacs 4.6.2 Compilation

Dear Justin and Mark Thank you for your Previous reply     Can i Use the Following Intel  Compiler  for grmacs 4.6.2 in centos Linux OS ? Intel® C++ Composer XE 2013 for Linux it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1, Intel® Math Kernel

[gmx-users] Reg error in Compilation Of Gromacs 4.6.2

Dear Justin Thank you for your Previous reply, I am trying to Install gromacs 4.6.2  in a cluster having centos OS with teh Following Command   I got following error cmake .. -DGMX_BUILD_OWN_FFTW=ON   -DGMX_MPI=ON  -DGMX_DOUBLE=ON CMake Warning at

[gmx-users] reg GPU Mdrun Error

respected  mark sir  , Thank you fro your previous reply When i run the production Mdrun  I have got the following error job is terminating with segmentation fault error Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.log to

[gmx-users] Reg Mpi run Error

Dear Jutin and Marks  Thnak you for your previous  reply Whrn i run the following job in cluster  as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr   -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the

[gmx-users] Reg mpirun error

Thank you justin for your reply The error I have pasted here (also pasted in previous mail) is total screen ouptut. No further output as you stated in previous mail( The real error is further up in the screen output or in the .log file.) [hinditron@compute002 gromacs-plumed-cpu-input]$

[gmx-users] About script for free energy calculation

Dear Justin thank you for your Previous reply   I am following your methane/water free energy tutorial I have Generated All .mdp files wiht Different LAMBDA value But When I Run job using Your Job.sh  script  in usr/local/gromacs4.6.2/bin I have Received the Following error  ( I ma running

[gmx-users] About Error in mdrun

Dear justin Thank you for your previous reply  When i run the md in gromacs 4.6.2 with plumed1.3   Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores   and the -pin option is set to auto: will not pin thread to cores.   This

[gmx-users] About running Production simulation in GPU with twinrange cut-off

Thank you Justin     To check Performance in GPU i Need to  run simulation  with same parameters for r coulomb =  rvdw   rlist        = 0.9        ; short-range neighborlist cutoff (in nm) rcoulomb    = 1.4        ; short-range electrostatic cutoff (in nm) rvdw        

[gmx-users] About Running production simualtion in GPU

Thank you Justin for your pervious reply                                                                 As you mailed me When using PME,   the rcoulomb is little bit fiexible and Validationof Modification is necessary .  But How to Validate Such Modification ?  i request you Humbly to give

[gmx-users] About running gromacs in GPU

Dear Justin Thank you for your previoue reply I have prepared a   .tpr file to run it run Successfully in CPU But when i use the Same .tpr files to run in GPU , It have not run successfully What is  reason ? What Command Should I give When I run .tpr file in GPU I  Hope it may be mdrun

[gmx-users] About Physical parameters

Dear Justin Thank you for your Previuos reply     I am using gromos53a6 ff When i changed the parameters for cut-off  (r list ) value to 1.2 I have got Error as follows  What is the Meaning of Note 2 3 NOTE 2

[gmx-users] About coulmb Vanderrwalls cutoff

Dear Justin Thank you for yoyr Previuos reply     I am using  Gromos96 53a6  so i am using  the following parameters ns_type = grid   nstlist = 5   rlist   = 0.9 rcoulomb    = 0.9 

[gmx-users] About coulmb Vanderrwalls cutoff

Dear Justin  Thank you for your Previous reply.                                                                              As yo mailed me  The Defaut      Value for vandewalls and Electrostatics  in GROMOS96 53A6  is  PME option s_type    = grid  nstlist    = 5  rlist      = 0.9  rcoulomb 

[gmx-users] About coulmb Vanderrwalls cutoff

Dear Justin thank you for your previous reply                     How can i check using th value 1.4 is harmless to My system Through g_energy ouput (potential.xvg) can i check (graphically) Thnaks In Advance -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] About Concatenation of several trajectory files

Dear Justin, Mark other gromacs users Thank you fro your previuos replies     I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or  Is it enough to use cat command  in Linux Thanks In ADVANCE -- gmx-users

[gmx-users] Compilation error

Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving

[gmx-users] About Checkpoint error in gromacs 4.6

Dear Justin Thank you for your previuos reply   I am using gromacs 4.6 AMD 8 core processor When I run restart My run  from the Checkpoint file using the following error ./mdrun_d  -s CNTPEPRSOLNPT.tpr  -cpi

[gmx-users] About Checkpoint error in gromacs 4.6

Respected Erik Marklund,   Thank you for your reply When i run with a  -noappend option from the checkpoint it runs well but Ooutput files are in Different Names The files Are not merged (are not Continues) ./mdrun_d  -s CNTPEPRSOLNPT.tpr  -cpi

[gmx-users] About Checkpoint error in gromacs 4.6

Deat Justin Thank you for your Previuos Reply,                                                                     But When I Run tne the following command with Append Option mdrun_d  -s CNTPEPRSOLNPT.tpr  -cpi CNTPEPRSOLNPT_prev.cpt  -v -nt 8 -deffnm CNTPEPRSOLNPT -append I Have got

[gmx-users] About Compiler Option

Dear Justin and other gromacs users ,                                                                     Thank you for your Previous reply I  Have AMD Block Edition FX8350 Processor  Also I have Ubuntu 10.04 OS Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA

[gmx-users] About Compilation error in gromacs 4.6

Dear Justin Thank you for your Previous reply,     I have Downloaded gromacs 4.6 I have configured well using the following command cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d and

[gmx-users] About Warnings in Mdrun

Thank you Mirco Wahab and Other Gromacs users   As you Mailed Me I have compiled gromacs 4.6  I have installed using the command As posted in mail But I have AMD 8 Core black Edition When I run the mdrun I saw a warning

[gmx-users] About CNT wrapped by Cyclic peptide

Dear Mark and Justin  Thank you for yours previous  Replies; You Mailed ME that My NVT and NPT  equilibration is seems to be  crashed . But   Actually My NVT Equlibration and NPT Equlibation was Sucessfull It  gives Nice output  without Lincs  warning ,  System exploding  But My Question Is 

[gmx-users] About CNT cyclic PEptide

Dear Mark/justin Thank you for Previous reply My Final Production MD only shows Error Like Lincs , System Exploding  And segmentation Fault TO Avoid this May I Further Extend My equilibration from 2 ns to 10 ns ? Thanks in Advance -- gmx-users mailing list

[gmx-users] About Production MD run error

Dear Justin Thank you for previous reply.   I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide) After Successful  NPT and

[gmx-users] About Warnings and Note in Production MD

Dear Justin Thank you for previous reply.   I am doing Carbon nano tubes Wrapped by Cyclic peptide After NPT and NVT equilibration When i Run Production MD I have got The following Notes in terminal NOTE 1 [file

[gmx-users] Notes from Production MD

Dear Baptiste ,   Thank you for your reply I have checked Nothing Wrong in the corresponding atom environments also  if is  Bad contacts During Energy Minimization it shows error .BUT My EM was successful . I Think Equilibration is not enough How to check Whether My

[gmx-users] About Merging topologies

Dear Justin thank you for your reply, Is there is Any tool  to merge topology of CNT (generated by g_x2top tool)  and Cyclic Peptide ( created by pdb2gmx) . otherwise Mere copy and Pasting the Corresponding Entries of CNT ( atom, Bond

[gmx-users] About Topology construction for CNT wrapped by Cyclic peptide

Dear  Justin , Thank you for your reply,     I need to construct  Topology For Carbon Nano tubes (CNT) in  gromoff53a5.ff . For that  When i run the Following Command  ./g_x2top_d   -f CNT.gro   -o CNT.top  -r CNT.rtp  I have

[gmx-users] About CNT-CYCLIC PETIDE constructio

Dear Justin Thank you for your Previous reply, I would Like to Construct a system of Single walled Carbon Nano tubes (SWCNT) Which should be Wrapped by Assembly of Cyclic Peptide . it Means CNT should be inserted

[gmx-users] About Deutrium Order Parameter

Dear Justin Thank you for your Previous reply,  I want to calculate  Variation of deuterium order Parameter With respect to Time  for Entire Trajectory and Hydration Number of Phosphate oxygen For My Entire

[gmx-users] About Detrium order Parameter

Dear Justin Thank you for your Previous Reply   I am following you Protein Lipid Tutorial . In Analysis Part I  Have Done Deuterium Order Parameters Analysis using index files . Kindly  brief About Deuterium order

[gmx-users] About Check point for restart

Dear Justin Thank you for previous reply,   There is power cut when i run My simulation So My System Gets Automatically restarted (Due to Low ups Power Packing)  Then I want To restart My simulation using the obtained Checkpoint so

[gmx-users] error in md.log files

Dear Justin Thank you for your reply,   I have set the Restraint  Along the Z Axis .  as follows #ifdef POSRES_WATER  ; Position restraint for each water oxygen   [ position_restraints ]       i  funct      fcx        fcy        fcz       1    1        0          0      100   #endif

[gmx-users] Aout Restraint on Water oxygen atoms

Dear Justin Thank you for your reply, I have set the Restraint  Along the Z Axis .  as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen  [ position_restraints ]     i  funct      fcx        fcy        fcz    1 

[gmx-users] About Index Files

Dear Justin  Thanks you for your Previous reply     I am Following your  Lipid Protein Tutorial When I try to create  index File from .gro file obtained  After   genion EM (grompp) pro gramme   Then I have got  Repetition of Groups (from 1 to 11 11 to 21) in

[gmx-users] About Usage of Restraint

Dear Justin Thank you for your previous Mail Reply      As you Instructed me in the Previous Mail  to insert Vertical Restraint I Have increased  Value

[gmx-users] About the Diffusion of Water Molecules

Dear Justin Thank you for your Previous reply,         I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of  Cyclic Peptide ( Made up of Only Phenyl alanine Residue) in DPPC

[gmx-users] About Grid MAT

Dear  Justin Thank you for your Previous Reply Mail     I am using GridMAt MD Script When I run the APL Headgroup Calculation It runs well But  I Have got  Output With  the Following Comment in My Command Prompt looking for offending protein atoms... There

[gmx-users] About Lateral Diffusion of Lipids

Dear Justin Thank you for your Previous reply I am Following your Protein Lipid Tutorial When I do the msd analysis For  protein in DPPC lipid-water Bilayer in lateral Z direction  using P8 atoms as index  Then  I have Got the Following Output      Is the Following My  Out put is Reasonable

[gmx-users] About topology for cyclic petide

Dear justin     Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide  using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal  But When I interactively Choose the Terminal  By pdb2gmx  It Shows Only

[gmx-users] About construction of Cyclic peptide

Dear gromacs users I would Like to Construct a assembly of cyclic Peptide  Is there is Any On line server or Tools Available ? Or any other Package Available It would be helpful if somebody Assists me Thanks In Advanve -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] About Packing of Lipids

Dear Justin , Thank you For your reply   I am following your   Protein lipids Tutorial  . I have Reached APL 61.14 A^2   Then I did Em And NVT equilibration  . As stated in your Tutorial . But After  NVT Equilibration    When I visualize My .gro File in VMD  I have Observed

[gmx-users] About Diffusion of Water towards Protein in ceter of box

Dear Justin,    Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested  me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration

[gmx-users] About Diffusion of water Towards Tail part of Lipids

Dear Justin,   Than you for your Previous reply  Regarding Diffusion Of Water From Head of Lipids to Tail Part  During NVT Equilibration, You Suggested My one question  as follows May I freeze these molecules During NVT Equilibration) ? The better approach would be a

[gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration

Dear Justin,     Thank you for your previous reply,    I am  doing Protein-Lipid simulation. After Em When I visualize the str in .vmd  The water Molecules Present in Lipid (DPPC) Head groups .There is No

[gmx-users] About Box VEctor

Dear  Justin Thank you for your Previous Help Reply.                                                                                         I am Doing Protein Lipid Tutorial  I Have Done Successive  Shrinking (using inflate script) and EM until i reached APL (66.7 A^2) for  DPPC in protein

[gmx-users] About Box Vector

Dear Justin Thank you for your reply But For My system The Initial  Value of Box Size is (5 5 5) Not equal to Final Box Value in both X and Y dimension 6.81123   6.81123   5.0  May Increase the  Initial Box Size ? or otherwise

[gmx-users] About Usage of maxwarn option in EM Afer first first Shrinking

Dear Justin Thank you  For your Previous reply,       For My system   After First Shrinking Using Cut-off Value DPPC  18   perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat Then  I do the EM.During EM I

[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation

Dear Justin ,    Thank you for your Previous reply I am following your Protein Lipid Tutorial After  Several Shrinking and  several EM  of my  system   i reached the APL for DPPC 64am^2 , I Have Added the ions to Neutralize the system . Then I have Done EM When I Visualize

[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation

Dear Justin,    With your Permission May  I send the Equilibrated Structure  to your Mail ID in Kindly Give ME Some Suggestion  After Seeing my Structure? I am Eagerly Expecting your Positive Reply Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] About APL And Shrunken System Size

I gave My cmd Prompt output for  satisfactorily shrunken system  as follows  Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled

[gmx-users] About BoxVector and APL

As uou Told me in the Previous Mail I have Given My sereis of Commands With Real file Names   ./pdb2gmx_d  -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc  ./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c  ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3  -box 6 6 6  

[gmx-users] About Doubt in Lipid protein Solvation

Dear Justin Thank you For your Previous Kind Reply    I am following your Lipid-protein Tutorial  for My system   I  Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As

[gmx-users] About Box vector and solvation

 Dear Justin Thank you For you Previous reply.     When I use inflate script  There is Automatic  Change in the box Vector At the End line of .gro file (output of inflate script)   Then I have Done EM without Changing the

[gmx-users] About Keepbyz script for Deleting sol Molecules

Dear justin Thank you For your Previous reply,    I am deleting The Water Molecules using keepbyz script as mailed me I want to keep waters around the head groups of my lipid, so How to Choose wisely  upperz and lowerz

[gmx-users] About Removing excees Water molcules in Lipid Bilayer simulation

Dear justin, Thank you For your Previous reply I  am doing Lipid -protein  Bilayer simulation.  As instructed in your tutorial i Have done Shrinking And  EM .until i have Attained Area per Lipid 62.36A. Then I Have solvated  as in the Tutorial (  using Vadradii 0.375)  using

[gmx-users] About DPPC Cut-off

Dear justin Thank you for your previous reply,     Finally I Have Found out problem When I Shrink My system Using Script The Size of the box at the end of System_inflated.gro file is not as i Have Assigned previously   it

[gmx-users] About Solvation of Lipid Protein

Dear Justin Thank you for your Previous reply I am  following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial   How many   Number of Water Molecules  you  needed   to  solvate Lipid -protein 

[gmx-users] About Diffusion of Solvent Molecules

Dear Justin,   Thank you for your Previous reply. I am Extending your Protein Lipid tutorial To my System I am using DPPC128.pdb  Which Surround the Cyclic Peptide. As You Quoted in tutorial I am Solvating My Lipid-protein Environment Using 148 Molecules (By genbox tools

[gmx-users] About EM for Lipid Protein Tutorila

Dear Justin Sorry   for the inconvenience in the previous Mail . I am Much obliged for your  Previous help Now I  am following Your Lipid Protein Tutorial  I am using DPPC128.pdb And I Have Downloaded the DPPC.itp and topol_DPPC.top When I run the energy Minimization (em.mdp Downloded form your 

[gmx-users] About Em and Equlibration With Lincs Algorithim

Dear Justin Than you for your previous Reply  I am doing EM for My cyclic peptide using following EM. MDP ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator  = steep    ; Algorithm (steep = steepest descent

[gmx-users] About Lincs Algorithim for Cyclic Peptide

Dear Justin Thank you For your Previous reply    I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion Without using  Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though  I have reduce the time step     relative constraint deviation

[gmx-users] About Usage of Constraints

Dear justin Thank you for your previous reply     I  am running NPT Equlibration  at 20 ps  with dt 0.0002 in 10 steps  Without usage of  Lincs Algorithm and its related parameters it runs Successfully . But When I  Increase

[gmx-users] About Protein in Bilayer Simulation

Thank you Justin For  Your Previous reply Finally Somehow I have  Adjusted  The Cut-Off  and  Grid Size and Inserted Protein in Lipid By Deleting some Lipid Molecules  MY Question is  1)  When I am Using inflategro  Perl  Script ,I

[gmx-users] About pritein Lipid Bilayer Simulation

Dear Justin , Thank you for your Previous reply using Genbox I have  Successfully Solvated  Energy Minimized  System_shrink.gro file  It adds 84266 water molecules .  Then  Tutorial How to Check Existence of Water Molecules within HydroPhobic  core of Bilayer  it is 

[gmx-users] About Lipid Protein simualtion

Dear Justin , Thank you for you Previous reply.  I am doing  Simulation of Cyclic Peptide in Lipids  I am following your tutorial  When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows  .

[gmx-users] About Warning in grompp

Dear  Gromacs users    i am doing NPT Eqlibration for a cyclic peptide When I run grompp I have got Warning as follows  WARNING 1 [file 2KDQ3.top, line 1137]:   The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has   an estimated

[gmx-users] About Bond in Topology

Thank you Sir. For your repl I Would like to construct .top file for Cyclic Peptide . My N-terminal residue is ARG  and C-Terminal is  PRO .  In pdb There is Bond between N atom of ARG (First residue)  and C atom  of  PRO (Last Residue) When I Generated Topology using pdb2gmx .  But  there is

[gmx-users] About Presence of Bond In Topology

Dear Justin Thank you for your Reply After pdb2gmx When i Visualize the resultant .gro file  of  my cyclic peptide in VMD I have Observed the Bond Between  Nitrogen atom (N ) of First residue and Carbon atom (C) of Last residue   I have not observed The same bond when I open and Visualize

[gmx-users] About Energy Minimisation

Dear  Mark Thank you for your previous help   With your Help I Have successfully Constructed .top and .gro for my cyclic peptide  After That i Have solvated and  added ions . . But when I do Energy Minimization  My Molecule after Energy

[gmx-users] About topology construction for yclic pepetide

Dear Mark ,   Again    Thanks  for you reply After Editing my pdb  file from intial FL to FLF format  Then i Run pdb2gmx for my linaer    pdb  file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as

[gmx-users] About topology construction for Cyclic peptide

Dear Mark,   Thank you for your reply I have used the peptide  FLF For that  pdb2gmx construct topology successfully with -ter  choosing any thing  for both terminal. But When i Choose none with -ter for both terminal It  again shows error as follows Fatal error: There

[gmx-users] About EM for Cyclic Peptide

Dear Mark Thank your excellent and patience Reply. it is very useful I Did as you Instruct in Gromacs Mailing List But when I DO Energy Minimization I have got following error Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential

[gmx-users] Pdb2gmx for cyclic Peptide

Dear Justin Thanks Again for your reply   When I run  Pdb2gmx using -ter option for my Cyclic peptide and i have selected None for both termini as you instruct in the previous mail i have got error as follows Fatal error: There is a dangling bond at

[gmx-users] About pdb2gmx for cyclic pepetide

Dear Justin  and other Gromacs users ,     Thank you for your previous reply    Again i Have tried  the option -missing when i use pdb2gmx tool i have got errror as follows My command is ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top  -missing -ignh -ter There is a

[gmx-users] Reg pdb2gmx for Cyclic peptide

Dear Justin Thank you for your Previous reply,    sorry for the inconvenience  to you personal Mail. I am doing MD  Cyclic Peptide  When I run  pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not

[gmx-users] About Bond breaking and usage of constraints

Dear justin ,     Thank you fro your Reply   I am doing MD for  Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal .  I have run pdb2gmx it is oak.  . I have solvated and added ions successfully But when i Run the Energy

[gmx-users] About Number of Components of eigen Vector

Dear justin Thank you for your gem of Reply  I am doing ED. With respect to my all  900 C-alpha atoms So I have used the output of g_covar namely eigvec.trr  as input to g_anaeig_d  as follows g_anaeig_d  -v eigenvec.trr -comp eig1.xvg -first 1 -last 3 -xvg none I have obtained eig1.xvg  i

[gmx-users] About Shake and Lincs Algorithm

Dear Justin ,    Thank you for your Previous useful  reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1  with  continuation = yes Is it Correct to use two algorithm  for simulation of

[gmx-users] (no subject)

mdout153.mdp  /dev/null mpirun -np 4 $MDRUN -deffnm 232npt153 /dev/null #exit Thanks in Advance  With Regards S. Vidhya sankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive

[gmx-users] About EM Error (simulation exploding)

Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in   gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm These are ignored for the rest

[gmx-users] About EM

Dear gromacs user,     Thank you for your previous reply. i am doing  Energy minimization  using Steepest Descent method . When i do that i got the following error r Steepest Descents converged to machine precision in 35 steps, but did not reach the requested Fmax

[gmx-users] About pdb2gmx

Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro  -p 1OG2O.top   -renum It runs successfully. But i have on issue. My PDB contains  HIS residues in both chain A and B I have selected  GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) The .rtp

[gmx-users] Mopac gomacs installation

Dear Gromacs user     I am trying to install Mopac gromacs . i have folloed the instruction as in the web page I used the following command LIBS=-lmopac   LDFLAGS=-L/usr/local/lib   ./configure  --with-qmmm-mopac --enable-double --program-suffix=_d It configured

[gmx-users] jalem...@vt.edu

Dear Justin Thank you for your previous reply  How to solve error obtained when i invoke  command as follows   ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh caught-output.txt   I got error as follows in Caught_output .txt File ./setupUmbrella.py, line 182, in module out = main()

[gmx-users] About Mike Harms python script

Dear justin  Thank you for your previous reply   I am doing  Umbrella sampling in gromacs I have 30 set of initial configuration in .gro file format .Now i would like to do NPT equilibration and  umbrella sampling for all these configuration  (for these i have to carry out 30

[gmx-users] About Umbrella sampling

Dear justin Thank you for your previous Valuable reply.   To do umbrella sampling  should i  run more number of steps than i run in Umbrella pulling ?   otherwise if i use lesser number of steps in Umbrella sampling than

[gmx-users] About gomacs MPI installation

Dear justin    Thank you for your previous reply Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of all i have successfully installed debain package of  gromacs-openmpi for that i have configured and  compiled using the following command ./configure 

[gmx-users] About usage of node in mpi calculation

Dear justin ,   Very very thanks for your previous patience reply When i run the mpi calculation using more than one node  (each node have 16 processor)  which option do i need to use in the following command  may i use -npme option? mpirun  -np 19  mdrun_mpi_d  -s toplo.tpr Thanks

[gmx-users] About Umbrella spacing

Dear justin thank you for your reply. i Have got Summary_distance.dat file as output  I need 0.02 nm Spacing For that I  Inspect Output .Dat file For some Distance i Have not obtained corresponding Coordinate files Example  as follows 

[gmx-users] About Distance.pl script

Dear justin , Thank you for your previous reply When i Download and  run Distance.pl script In your website I got the following error readline() on closed filehandle IN at ./Distance.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at ./Distance.pl line 30. How

[gmx-users] About desired Spacing in Distance.pl script

Dear justin Thank you for your at once reply       I have successfully use the Distance.pl I got output. .But in Distance.pl script i have not represented the Any  Desired spacing (0.3nm) . Should i Represent? . If  i need to

[gmx-users] Abot genbox and editcon

Dear justin Thank you for your previous reply   I have solvated  my protein molecule with specific number of water molecules By keeping the protein (solute) at center of box (option available in editconf)  but when i visualize the resultant  .gro

[gmx-users] genbox

Hello  Justin, Thanks for your patient reply      I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ?  in editconf with regards S.Vidhya sankar -- gmx-users mailing list

[gmx-users] About solvation

Dear Mark   Thank you for your reply.    I did As u said  But when I visualize  the resulting .gro files in VMD  .The solute molecules are centered (i used the center option in editconf) But solvent molecules are are away . but within the box i need Solute 

[gmx-users] About spacing in umbrella sampling

Dear justin, Thanks for your previous reply which one is reliable  to get desired spacing in umbrella sampling either from output of  g_dist or from  pullx.xvg? If i choose spacing from pullx.xvg will it affect the result ? (poor  sampling and poor free energy calculation). Thanks in

[gmx-users] About restraints

Dear Plumed gromacs user Does any body know  How to set  restraint suitably  in umbrella sampling using plumed -gromacs ?   i am using plumed for umbrella sampling Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] about umbrella sampling

Dear Justin, Thank you for your immediate reply amidst of your busy schedule I  am trying to pull one of  chain of my protein   using umbrella option of gromacs (As did in your website tutorial)  After umbrella  pulling i have extracted all frame of .gro  from .trr files .

[gmx-users] About Choice PDB

Dear justin,,     Thank you for your immediate reply. Which PDB is suitable Either X-ray PDB  (brookavean protein data bank) or NMR PDB  to study the effect of ionic strength on protein. If i use x-ray PDB will it affect the result though i solvate and neutralise the PDB before

  1   2   >