[gmx-users] Salt bridge calculation using GROMACS analysis tools

macs-user.biotalk.us/salt-bridge-calculations-t91121.html Then there is the "g_saltbr" tool. I am confused now as to what to use. If I want to use "g_dist" how should I proceed ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailin

Re: [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

Hi Antara Did you check the plot of the potential energy against the simulation time ? You can visualize the convergence of your energy minimisation from the above plot. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On 2/9/15 7:41 AM, Antara mazumdar wrote: > i

[gmx-users] Umbrella Sampling and histograms smoothness

: ​ HISTO <https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web> ​ Kindly help. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/G

Re: [gmx-users] Umbrella Sampling and histograms smoothness

"restraint forces" for DNA/protein systems ? Regarding window setup, is it the spacing of the windows ? Except for simulation time is there any other method for increasing sampling ? I have read the manual but could not find anything. I am searching in the web also. Thanks & Regards Agn

[gmx-users] Umbrella sampling restraining potential

the 12600 units of force constant as it is very high and there is no validation. I found some literature using 1000 - 10,000 kJ/mol/nm^2 force constants for proteins. Any suggestions please ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing

[gmx-users] Umbrella Sampling and Histogram

drive_web> ​ I think the shape of the histograms is OK now, they dont appear rocky and broken. I suppose I need proper overlap at present with regards to window spacing and all. Kindly review and suggest. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Us

Re: [gmx-users] Umbrella Sampling and Histogram

e and error ?? On 2/19/15 9:50 PM, Agnivo Gosai wrote: > Dear Users > > This is my earlier post wherein I received useful suggestion from Dr. > Lemkul. > > http://comments.gmane.org/gmane.science.biology.gromacs.user/74659 > > Earlier for my system , I was doing a

Re: [gmx-users] Umbrella Sampling and Histogram

e PMF converged from the standpoint of error analysis. What are your opinions ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads

erv_pmci.c:388): error waiting for event [mpiexec@node094] main (./ui/mpich/mpiexec.c:718): process manager error waiting for completion Can anyone please help with this I am waiting for a reply in this forum after which I will take it up with the cluster admins. Thanks & Regards Agnivo Gosa

Re: [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads

I think it is well explained and should work with GROMACS 4.6.7. Any suggestions ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Ca

Re: [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads

ore nodes. However there is no output when np = 24 or 32 and such like. I dont get what is going on. I have contacted my university HPC group and described the problem. Lets see what happens. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list *

[gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads

trator. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscr

[gmx-users] Re : Re : GROMACS 4.6.7 not running on more than 16 MPI threads

/ns) Performance: 21.3931.122 So , I have bad performance. Now I am using only MPI for running the jobs. Any suggestions on performance improvement ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archiv

[gmx-users] Creating POSRES option for MDP file

ing simulation ? Or there is some other method ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.grom

[gmx-users] mdrun blowing up with PME node error in 1 window of umbrella sampling

advisable ? Kindly suggest. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Maili

Re: [gmx-users] mdrun blowing up with PME node error in 1 window of umbrella sampling

results seem to match published literature. So I am happy. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Wed, Mar 4, 2015 at 2:38 PM, Agnivo Gosai wrote: > Dear Users > > I am using umbrella sampling to calculate free energy of binding between > two biomolecu

[gmx-users] Using thermostats to create temperature gradient in system

motion removal for the whole system. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.or

Re: [gmx-users] Using thermostats to create temperature gradient in system

thermostat , GROMACS will give error message. So how do I fix this problem ? Or, should I freeze the protein instead and use a thermostat on the solvent ? I am trying both of these as I write this mail. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing

Re: [gmx-users] Using thermostats to create temperature gradient in system

Best, Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)sub

Re: [gmx-users] Using thermostats to create temperature gradient in system

error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Using thermostats to create temperature gradient in system

. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un

Re: [gmx-users] Using thermostats to create temperature gradient in system

comm-mode = Linear comm-grps = System Plz have a look. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

Re: [gmx-users] Using thermostats to create temperature gradient in system

Dr. Lemkul Thanks for such an easy fix to my problem. I guess I have been doing all sort of weird stuff since last night instead of thinking logically and reading the relevant portion of the manual. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mai

[gmx-users] NVT Equilibration error

or e.g.) and then do a NVT equilibration at 300 K? Kindly suggest. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Re : NVT Equilibration error

input.pdb -o complex.gro -p topol.top and I use AMBER99SB ( with parmbsc0 for the DNA part ) , TIP3P water. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

Re: [gmx-users] NVT Equilibration error

input.pdb -o complex.gro -p topol.top and I use AMBER99SB ( with parmbsc0 for the DNA part ) , TIP3P water. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

Re: [gmx-users] NVT Equilibration error

Justin & Tsjerk So, do you think the equilibration error is because of this long bond ? I was thinking as the error message was about water molecules/atoms , the source was something else. I will get back after I fix this warning in a proper and acceptable way. Thanks & Regards Agni

Re: [gmx-users] NVT Equilibration error

docs.google.com/file/d/0B-U8uULVZjfRQ0JzdVZlcG1YWjQ/edit?usp=drive_web> ​ For the 1st image VMD did not show the secondary structures of the protein as a STRIDE warning and error came. However the energy minimized structure did not show such warnings. Any suggestions Thanks & Reg

Re: [gmx-users] NVT Equilibration error

229 and 230. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lis

[gmx-users] Re : NVT Equilibration error

Dr. Lemkul, Thank you very much for taking time to review my problem. I am sure this forum post will help all the new members in resolving related issues. I will post again after attempting another equilibration. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gro

[gmx-users] Problem with xpm2ps

other software like Adobe / Inkscape to edit the image? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.grom

[gmx-users] Fractional charge for protein after topology preparation

rstand the fractional charge for the protein. Any suggestions ??? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] Choosing LINCS setting / rcon for parallel mdrun

interpolation fourierspacing = 0.12 ; grid spacing for FFT I would still like to use 64 processes for the mdrun. Any suggestions please. I am thinking of playing with -rcon. But I am not sure if it will affect the accuracy of the simulation. Thanks & Regards Agnivo Gosai Grad Student,

Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun

to equilibrate more ? I used AMBER99SB/TIP3P. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Mon, Nov 16, 2015 at 1:49 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > groma

[gmx-users] How to get a compressed pull force output from SMD simulation ?

.xtc file so that the pull force and the COM separation are of same vector lengths? or do I need to add something to my .mdp file to be able to do it ? Like , nstfout ?? I did not download the trr file from the cluster as it is very huge ! Kindly help please. Thanks & Regards Agnivo Gosai

[gmx-users] MDRUN warning during minimization

-extension distance in the mdp file if you are really sure that is the reason. I am seeing this for the 1st time , kindly help in understanding. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

[gmx-users] Placing water molecules in a defined space in the model

tps://drive.google.com/file/d/0B-U8uULVZjfRaUhmNXB0RU9rZk0/view?usp=drive_web> ​ Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] MDRUN warning during minimization

; Include [atomtypes] #include "myligand_atomtypes.itp" ... So should I look at the parameters for AMBER99SB ?Kindly suggest. Thanks & Regards Agnivo Gosai Grad Student, Iowa State U

[gmx-users] Using make_ndx to combine many residues into 1 group

n or shell script ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Using longer cut-off for AMBER99SB

r comments then do I need to show equivalent simulation data as in the original ff paper. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

[gmx-users] Meaning of the screen output "largest charge group radii "

cut-off of 0.8 nm for all non-bonded interactions. Please explain. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Trajectory correction for pbc before H-bond analysis

, I was thinking if I could skip that step for now. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Calculating avergae structure from the simulation

ocedure to conduct the simulations.But now I am confused. Kindly comment. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] How many times should I do Umbrella Sampling

simulation and the result is almost identical. I think as my pulling code is same I am getting more or less same result. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

[gmx-users] Lysozyme-Water Tutorial problem : em.tpr

, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>* - I am not sure as to how to carry on to the next level. Any insight is very much appreciated. Best Regards, Agnivo

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 124, Issue 40

Dear Dr. Justin Thank you for the insight . My problem is solved. Best Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University On Sat, Aug 9, 2014 at 5:00 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mai

[gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

64-Bit Could anyone please tell me what version of GROMACS I should try installing ?? Thanks & Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

[gmx-users] Using GROMACS to find the net charge on a Protein

the topology file generated by "pdb2gmx" contains the total electron charge value for a molecule. I was wondering if this can be used to get the charge value for Thrombin at physiological pH. Thanks & Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State Universi

[gmx-users] Compiling GROMACS 4.5.6 in Cluster

Dear Users I am facing a problem while compiling the GROMACS source code in my university cluster. I am laying down my installation procedure step by step :- 1. Downloaded fftw 3.3.4 2. exported paths of C-compiler and Fortran-compiler 3. Used the following command line to configure FFTW *./confi

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 125, Issue 59

721 (2005)) > > You should look if the pH, which you need, is > o < that the corresponding > value of pka and then you should determine the protonation state of the > protein . The pdb2gmx program has the option of being interactive with > respect to those aminoacids that h

[gmx-users] Problem Compiling mdrun parallel version for GROMACS 4.5.6

Dr. Lemkul Thanks for your valuable suggestion. I used make distclean and could successfully install the serial version of GROMACS 4.5.6 in my university cluster After that I used "make distclean" again and proceeded with compiling the parallel version of mdrun in a separate directory However wh

[gmx-users] Understanding comments in pdb2gmx output

Dear Gromacs Users I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO ) . I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported into it. I had cleaned the PDB file off crystal waters and a small chemical ligand ( which I dont require ) before passing it t

Re: [gmx-users] Understanding comments in pdb2gmx output

er of residues have increased and the total no. of atoms have also increased.* *I have also observed the same thing while completing Dr. Lemkul's tutorials. Why does this happen ? I have searched the web but could not find any satisfactory answer.* Thanks & Reagrds Agnivo Gosai Graduate Student Iowa

[gmx-users] grompp fatal error in GROMACS version 4.5.7

also consulted the error section of the GROMACS documentation but could not understand. Thanks & Regards, Agnivo Gosai Grad. Student , Iowa State University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] Understanding g_energy output in GROMACS 4.5.7

meaning of the term "Err. Est" and "Tot-drift". I have consulted the GROMACS manual but I am not satisfied and failed to understand the physical significance. Kindly explain. Thanks & Regards Agnivo Gosai Grad. Student, ISU -- Gromacs Users mailing list * Please sea

[gmx-users] Selecting box dimension and COM position - Pull Code

lated." Are there any guidelines for assigning the COM position of my biomolecule complex and the x,y,z dimensions of my simulation box keeping in mind the above explanation. Or I should go about it in a trial and error basis? Thanks & Regards Agnivo Gosai Grad Student, Iowa State Universit

[gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul

t the end? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

[gmx-users] Using make_ndx to couple molecules before pulling simulation

cture / coordinate ) file and named the DNA chain as Chain_D and the two protein chains as Chain_P. I believe that this is the correct approach before I run the pulling simulation. I request the experienced users to suggest and comment on my understanding. Thanks & Regards Agnivo Gosai Gra

[gmx-users] The last line in a .gro file

file having the vectors listed in the last line. My question is :- Is the last line has to do anything with the "size" of the molecule ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.groma

[gmx-users] Understanding the results of NVT simulation

4.5.7 single precision. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mail

[gmx-users] NPT Simulation average pressure lower than Reference set pressure

set pressure. *So should I carry out the simulation for a longer time ?? Or should I use a different barostat on the next NPT run or do it in a fresh NPT run.* *Kindly suggest.* Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the

[gmx-users] mdrun error message in Computing Cluster

suggestions please ?? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lis

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

to achieve the reference set pressure. *So should I carry out the simulation for a longer time ?? Or should I use a different barostat on the next NPT run or do it in a fresh NPT run.* *Kindly suggest.* Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs U

[gmx-users] Umbrella Sampling Tutorial Question

PMF based on binding energy. Kindly shed some light on this issue , please. Pardon for my ignorance. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure

kMXNoYW8/edit?usp=drive_web> ​ Could anybody suggest why the reference pressure is not being reached ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users

[gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover

hainlength reset to 1 My question is how will this affect my simulations ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

Re: [gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover

protein complex as discussed in similar posts in the gmx forums. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Mon, Nov 3, 2014 at 6:37 PM, Agnivo Gosai wrote: > Dear Users > > I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using > GROMA

[gmx-users] Position restraining protein during equilibration stage

& Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] Position restraining protein during equilibration stage

during the production run ? Kindly explain. My reasoning so far is inferential , but I am searching literature on this matter. On 11/4/14 5:37 PM, Agnivo Gosai wrote: > Dear Users > > I have followed several GROMACS tutorials , specially the excellent Lemkul > tutorials. I have seen

[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

provide suggestions. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mail

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster On 11/7/14 4:20 PM, Agnivo Gosai wrote: > Dear Users > > I checked and found that the CMAKE version installed in my university > cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher. > So I installed

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

.kth.se> Cc: Date: Sat, 08 Nov 2014 09:19:14 +0800 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster What he meant was to specify full path of your cmake, i.e. /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY. (and so on); instead of just typing cmake .. -DGMX_FFT

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

http://lmgtfy.com/?q=difference+between+gcc+and+g%2B%2B http://lmgtfy.com/?q=gcc+compiler+installation+linux < https://mail.google.com/mail/u/0/?ui=2&ik=4d6c0a5051&view=att&th=149643f024d7d537&attid=0.1&disp=safe&realattid=f_i1wzdfrg0&zw > On Sun, Nov 9, 2014

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

;&1 | tee make-install.out > and share the resulting make-install.out file (use pastebin or similar). > > Cheers, > -- > Szilárd > > > On Sun, Nov 9, 2014 at 8:21 PM, Agnivo Gosai wrote: >> Dear Users >> >> I have tried installing both versions 4.6.5 and

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

it crashes it is installing in a directory which contains '/gromacs' about 300 times. My first guess is that you are installing in the same directory where your build (and source tree?) is. Is that the case? -- Szilárd On Mon, Nov 10, 2014 at 12:31 AM, Agnivo Gosai wrote: > Dear Users &

[gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

53454 atoms that were outside the box OMP: Error #178: Function pthread_getattr_np failed: OMP: System error #12: Cannot allocate memory Aborted Now upon searching on the web it seems to be an OpenMP error. Again I am in a fix which I have little or no idea about. Thanks & Regards Agnivo Gosai

Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

09 +0100 Subject: Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster On Mon, Nov 10, 2014 at 2:17 AM, Justin Lemkul wrote: > > > On 11/9/14 8:15 PM, Agnivo Gosai wrote: > >> Dear Users >> >> Firstly thanks (specially Drs. Szilard and Mark ) for helping me o

[gmx-users] Understanding Force Plot in Umbrella Sampling Simulations

in the GROMACS manual , however I would hugely benefit from the suggestions by the forum members. Thanks & Regard Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

[gmx-users] How to use make_ndx in script to combine 2 groups

interactions on a script. Can I type group1 , group4 , | , q on a .txt file and pass it onto make_ndx in the script. I have not seen myself , but I am speculating. Please bear with my ignorance. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing

[gmx-users] Problem mdrun_mpi GROMACS 4.6.1 in Intel Cluster

i from version 4.6.1 has not been properly compiled to run on several nodes in the cluster. However I would like to do it to speed up my simulations. Any suggestions , please ?? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Forwarded message -- From: Mark

[gmx-users] Umbrella Sampling Results and Issues

hould I simultaneously increase my simulation time for umbrella sampling to say 5 ns from 1 ns ? Kindly suggest ---- Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list *

[gmx-users] Umbrella Sampling and Electric Field

; Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe reques

[gmx-users] SMD - Pulling Error in mdrun 0.49 times box size

tal pulling distance) > 0.49 times 15 nm ( length of box in z direction ) and is contributing to the error. But this has been the same in cases 1 and 2 also. Hence I am getting confused. Any suggestions , please ?? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs U

Re: [gmx-users] SMD - Pulling Error in mdrun 0.49 times box size

Forwarded message ------ From: Agnivo Gosai Date: Tue, Nov 25, 2014 at 1:44 PM Subject: SMD - Pulling Error in mdrun 0.49 times box size To: gromacs.org_gmx-users@maillist.sys.kth.se Dear Users I have put my molecule complex in a box having dimensions 7.5 7.5 15 . The center of the molecul

[gmx-users] default state of "energygrps" in .mdp file

;energygrps" in a .mdp file. I checked the mdout.mdp generated during grompp+mdrun and found that energygrps = (blank). In that case what is happening ? I use version 4.6.7 and also checked the manual but could not satisfy myself. Kindly answer. Thanks & Regards Agnivo Gosai Grad Studen

[gmx-users] g_wham 4.67 version output query

/0B-U8uULVZjfRMVRINHNQOURCOWc/edit?usp=drive_web> ​​ PMF2.png <https://docs.google.com/file/d/0B-U8uULVZjfRWXdXVGVlNXU3Rm8/edit?usp=drive_web> ​​ pmfintegrated.png <https://docs.google.com/file/d/0B-U8uULVZjfROVBaaGlxWThZdEk/edit?usp=drive_web> ​ Kindly explain the possible reason behind this. Thank

Re: [gmx-users] g_wham 4.6.7 version output query

meone say what is going on. Lookwise the pmfintegrated.xvg is so smooth that I am tempted to use it , but I don not know why and how it is generated. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Mon, Dec 8, 2014 at 11:35 AM, Agnivo Gosai wrote: > Dear Users >

[gmx-users] Calculating hydrogen bonds between specific residues

my system. I neutralized the system with Na and Cl ions such that the final conc is 0.1 M. b) In general is my procedure a correct way of using "g_hbond" ? Kindly help. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please sea

[gmx-users] Using do_dssp with GROMACS 4.6.7.

(8) ./dssp-2.0.4-linux-i386 -i pull1.pdb -o pull1.dssp This works fine. But I want to use GROMACS to generate plots and figures with its do_dssp command. Kindly help me to find a solution. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Pl

Re: [gmx-users] Using do_dssp with GROMACS 4.6.7.

Hello I am sorry for wasting your time. The online GROMACS help is enough to fix my problem. I am giving it below. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp The problem is fixed now!! Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Thu, Jan 29,

[gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand

cropped up in my mind. Do I need to provide an index file containing only the hydrophobic residues of the protein and the ligand ? Or, just a normal index file with all the protein residues and ligand residues in two separate groups will do the job? Thanks & Regards Agnivo Gosai Grad Student,

[gmx-users] A quick question regarding topology generation

ucture but still I am not able to figure out an answer to his question. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] pdb2gmx question - protonation

there any literature available. I am sorry if I am asking for too much. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't p

[gmx-users] H-Bonding residues against specific frames

was thinking of extracting every frame (using trjconv) from my total of 501 frames and running g_hbond on each of the frames. But that seems to be a laborious process. Is there any way out ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing