[gmx-users] Re:Re: Re: Average box size

27;t post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > >

Re: [gmx-users] Re:Re: Re: Average box size

; If Box-X Box-Y Box-Z represent average value of  a b c then volume >> >>> does not correspond to my triclinic box because its just >> >>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me >> >>> which volume should I consider for next NVT productio

[gmx-users] Question

Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: What

Re: [gmx-users] Sampling windows

Hi Xavier Thanks very much for your time. That has mad things very clear Gavin Avier Periole wrote: > > On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote: > >> Hi Xavier >> >> Many thanks. Two more quick questions (both refering to barrier region): >> Does the value of the force constant affect th

[gmx-users] Re: [ atomtypes ] are not case sensitive?

Dear GMX list, It's more the 2 years ago and now with my gmx.top file containing: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 caca 0. 0.

[gmx-users] methanol simulation

Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven

Re: [gmx-users] methanol simulation

On 6/01/2011 10:35 PM, mustafa bilsel wrote: Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I

Re: [gmx-users] Question

Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break

Re: [gmx-users] Question

On 6/01/2011 8:28 PM, Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of c

Re: [gmx-users] Question

On 6/01/2011 8:28 PM, Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of c

Re: [gmx-users] so difficult problem

Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother ye

Re: [gmx-users] so difficult problem

Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by t

[gmx-users] methanol simulation

Dear Mark, so, what should I do? mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list.

Re: [gmx-users] methanol simulation

mustafa bilsel wrote: Dear Mark, so, what should I do? In the future, it would be helpful to reply to the original thread instead of starting a new one. You said you added a line "SOL 291" to your [molecules] directive. That would imply that you named your methanol [moleculetype] SOL.

[gmx-users] methanol simulation error

Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CM

Re: [gmx-users] methanol simulation error

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011. For all questions about CloudBroker, please contact the compan

Re: [gmx-users] methanol simulation error

mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it g

Re: [gmx-users] methanol simulation error

On 7/01/2011 12:31 PM, mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp

RE: [gmx-users] methanol simulation error

Please copy and paste in here the contents of your .top file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

[gmx-users] trjconv with multiple chains problem

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 som

Re: [gmx-users] trjconv with multiple chains problem

yuanyuan wang wrote: 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,

[gmx-users] trjconv with multiple chains

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 som