[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

[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

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

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

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 jalem...@vt.edu wrote: On 10/28/13 7:41 PM, Hari Pandey wrote: Thank you so much  Mark. I still did not understand. More detaily.  Atomtypes

[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] Reverse_MICELLEFatel 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

[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] 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] 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

[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] 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] (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] 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