[gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4

Dear Gromacs users, Please somebody help . editconf computs the incorrect value of  "mass of input".  I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp.  The mass of

[gmx-users] (no subject)

Dear Gromacs users, Please somebody help . editconf computs the incorrect value of  "mass of input".  I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp.  The mass of

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

p is there and which contains the atom names  which I posted last email Thanks for your regard Hari On Monday, October 28, 2013 4:50 PM, Justin Lemkul wrote: On 10/28/13 7:41 PM, Hari Pandey wrote: > > > > > Thank you so much  Mark. > > I still did not understand. Mo

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

Thank you so much  Mark.  I still did not understand. More detaily.  Atomtypes are only following: atomtypes.atp:: H       1.00800 ;       polar H DUM        0.0 ;       dummy atom HAL1       1.008000 ;      alphatic proton HAL2       1.008000 ;      alphatic proton HAL3       1.008000 ;

[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

Dear Gromacs Users, First, I would like to thank Dr. Lemkul for reply. My problem description is as follows: I am using CHARMM36  forcefield to equilibrate of AOT. when I add the mass of all atoms from topology, it gives me 444.5 which is correct but when I run the script editconf -c  -f A.gro

[gmx-users] How To SOLVATE

Hi GROMACS users can any body tell me how do I solvate fixed number of molecules in fixed volume: for example 100 molecule water in 14*14*14 Aungstrom^3  box.  eidt conf and genbox  never can do this. One more question. Please any body help me on following warning: WARNING: masses and atomic (

[gmx-users] pulling along hexane-water interface

yed a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Ple

[gmx-users] (no subject)

ame thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.

[gmx-users] Reverse_MICELLE>Fatel error, moleculetype SOL is redefined

Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.     When I do grompp, it says moleculetype SOL is redefined and lo

[gmx-users] How do I make an AOT reverse micell, which package I should use

Hi all GROMACS users, I need to make a pdb file of AOT reverse micell . Please some body tell me how do I build it and which package would best for this work. Now I am using PACKMOL but it seems just a geometrical mathematical manipulation. I want to arrange charge, LJ parameter, hydrogen bond

[gmx-users] About Solvation dynamics

Hi GROMACS users, Could you please somebody tell me how do I solvate A Reverse Micell by fixed (200) molecule of water keeping in fixed annular region around it. That is how do I solvate spherical micell by water so that the width of spherical region around it is fixed? lots of thanks for help 

[gmx-users] new forcefield not appear in slave node pdb2gmx list

Hi all gromacs users, I have new forcefield and I have this folder in my working directory as well as in  /share/gromacs/top.  When I run pdb2gmx from head node this forcefield appears in list but when I run from slave nodes it do not appear in pdb2gmx list. could somebody tell me how do resolve

[gmx-users] about adding forcefield in the list of pdb2gmx

Hi all GROMACS users I added a new forcefield  folder to head node in /opt/bio/gromacs/share/gromacs/top  and it appears in the list of forcefield in pdb2gmx while I run it from head node of cluster. But if I run pdb2gmx from other slave nodes , it do not appear in the list. So, Please could

[gmx-users] Tempereture coupling and heat flux on each part

Hi all  gromacs users, I am new to GROMACS , please help me I have following (NVT.mdp) (NPT.mdp)  and (NVE.mdp)   .  I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. In gromacs I want to do Following:

[gmx-users] (no subject)

Hi all  gromacs users I have following (NVT.mdp) (NPT.mdp)  and (NVE.mdp)   .  I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps,  temperature of A and C should be constant (

[gmx-users] Decouple

Hi , How do I  solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for  B. Gromacs   display error, what is temperature for B. How do aI decouple part B thanks  for help Hari -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] OPLSAA.ff

Dear Gromacs users, I am a new user and I have some questions  I confused about indexing.  in atomtypes.atp  clearly  we can know the index is for what kind of atom but  in ffbondedtype.itp there is different kind of the indexing  so I confused how do i pathch the force field . Some are obvious

[gmx-users] write velocity and coordinates with template.c

in; charset=ISO-8859-1; format=flowed > > On 26/07/2012 8:22 PM, prithvi raj pandey wrote: >> Dear gmx users, >> >> I am using template.c of gromacs 4.0.7 for writing my own analysis >> tool. When I am using the fr.x[i][XX], it writes the coordinates of >> th

[gmx-users] Writing velocity of particles using template.c

Dear gmx users, I am using template.c of gromacs 4.0.7 for writing my own analysis tool. When I am using the fr.x[i][XX], it writes the coordinates of the particles (i crosschecked it with the coordinates written by the trjconv command). But the problem arises when I use fr.v[i][XX] for writing th

[gmx-users] Intermolecular RDF in DPPC

file /export/softexport/gromacs/share/gromacs/top/spc.itp Excluding 49 bonded neighbours molecule type 'DPPC' and does not proceed further. What is wrong? Can anyone please help? -- Prithvi Raj Pandey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] Problem with g_density

were done using the folloing tool g_density -f-o -n -s -d Z Can anyone help? -- Prithvi Raj Pandey -- 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

[gmx-users] help

-12837 with 2 bonds Can not find forcefield for atom OH2-12840 with 2 bonds Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 10110 out of 12941 atoms what should be the problem. and how can i solve it. Ashish Pandey NIPER India

[gmx-users] Hi

. -- Ashish Pandey NIPER India -- 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

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

Hello, Thank you for your reply. I used .tpr file genarated from grompp for mdrun which generated the .trr file. I have not specified xtc-grps. Regards, Nishtha On Sat, Jan 24, 2009 at 11:02 PM, Tsjerk Wassenaar wrote: > Hi, > > On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

wrote: > nishtha pandey wrote: > >> Hi, >>Thank you for your response. It is a protein molecule containing 610 >> amino acid residues. >> > > you didn't answer my question. > please inspect the molecular structure at the time point where the error &g

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

Hi, Thank you for your response. It is a protein molecule containing 610 amino acid residues. Thanks and regards, Nishtha On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel wrote: > nishtha pandey wrote: > >> Hello everyone, >> While trying to do the R

[gmx-users] g_rms: Too many iterations in routine JACOBI

Hello everyone, While trying to do the RMSD analysis of my trajectory file I am facing the error " Too many iterations in routine JACOBI". I have gone through the archives which suggests that such problem arises if there is mismatch between the reference structure and trajector

[gmx-users] LINCS warning in Position Restraint

Hi all, I am trying to position restraint on 1OMB.pdb using gromacs 3.2 I have included 2 CL- ion. My *.top is after editing: [ molecules ] ; Compound#mols Protein 1 SOL 1768 CL- 2 Am doing