RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

> Bo wrote: > Thanks David. So to speak, as the center of mass of group SOL is not > free to move, we do not need stopcm to it. Another question is, does > it would be problematic in long time simulation without stopcm in such > situation, I mean the systematic errors caused by center of mass > m

RE: [gmx-users] how to make choices of COM in the system with freeze group?

> > You can opt for 3). > > If your system only compose of nanotube and water, why freeze it? Thank Yang Ye, we are doing some tests on effects of T-coupling caused by removing COM in the system with freeze groups Regards, Yusong > > tuyusong wrote: > > > > Hi, all, > > > > > > > >

[gmx-users] about nmr refinement

dear users, I want to do a NMR refinement of a protein structure that comes from CYANA, (torsion angle dynamics), to include the interacctions betwen protein with the solvent, and improve the quality of the structure, my question is about the protocol that i should do, i have read the manual

Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

Thanks David. So to speak, as the center of mass of group SOL is not free to move, we do not need stopcm to it. Another question is, does it would be problematic in long time simulation without stopcm in such situation, I mean the systematic errors caused by center of mass motion. Thanks for clarif

Re: [gmx-users] structure files of water and CNT

> Hello, I am a new user of Gromacs and want to simulate water > transport through Carbon nanotubes. > > Where can I find structure files of water and CNT? Last summer I put a walk though with the basics for this. It can be found at: http://cs86.com/CNSE/SWNT.htm Although please note that this w

Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

tuyusong wrote: David wrote: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. yes. that should work. -Original Message- From: [

RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

David wrote: > you can not only remove the com motion of one group. it is all (in one > or more groups) or nothing. Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED

Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -

RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] O

Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps =

[gmx-users] Warning message with 3.3.3 but not with 3.3.1

Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t

Re: [gmx-users] structure files of water and CNT

Quoting Hero <[EMAIL PROTECTED]>: > Hello, I am a new user of Gromacs and want to simulate water > transport through Carbon nanotubes. > > Where can I find structure files of water and CNT? I believe there is an online server for generating CNT structures; check the list archives thoroughly and y

Re: [gmx-users] Conformation Search with Gromacs

Tandia, Adama wrote: Dear USERS, Can one use Gromacs for conformation search? If yes, how? If you mean systematic search the answer is no. You can do energy minimization or MD. Thanks, Adama _ Adama Tandia Modeling & Simulation Corning INC SP-TD-01-

[gmx-users] structure files of water and CNT

Hello, I am a new user of Gromacs and want to simulate water transport through Carbon nanotubes. Where can I find structure files of water and CNT? Thank you so much! Be a better friend, newshound, and

[gmx-users] Conformation Search with Gromacs

Dear USERS, Can one use Gromacs for conformation search? If yes, how? Thanks, Adama _ Adama Tandia Modeling & Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___

Re: [gmx-users] how to make choices of COM in the system with freeze group?

You can opt for 3). If your system only compose of nanotube and water, why freeze it? Regards, Yang Ye tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only re

Re: [gmx-users] how to make choices of COM in the system with freeze group?

I'm not sure that I interpret your question correctly, but my guess is that you want to remove the center-of-mass translation and/or rotation. You can set this in the .mdp file with the commands comm_mode and comm_grps and an appropriate index file. Please refer to the manual or the online

[gmx-users] How constraint structure not conformation

Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was think

[gmx-users] how to make choices of COM in the system with freeze group?

Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of "system" as a who

[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration

Oh dear, yes I do use a soft core potential and I overlooked that I set sc-power to 1. So even at lamda=0 there should be a soft core contribution to dV/dl! Thanks Berk. >I guess you are using soft-core interactions. >In that case there are more terms in dV/dl, see eq. 4.120 in the manual. Berk.

RE: [gmx-users] Error in topology file

This will be helpful for you: http://wiki.gromacs.org/index.php/Exotic_Species and other information from gromacs wiki. Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of s lal badshah Sent: 16 April 2008 11:12 To: gromacs Subject: [gmx-users] Error in topology file Dear Ex

[gmx-users] Error in topology file

Dear Experts, Hi ! I am doing simulation of cholera toxin, one with GTP( guanosine triphosphate) and other without it.The without GTP MD simulation I have done, now I started the other and when I used the pdb2gmx command on pdb file it says: Program pdb2gmx, VERSION 3.3.1 Source code file: resall

Re: [gmx-users] about specbond

Rui Li wrote: Dear all, I'm trying to run a simulation of a ligand bound to an enzyme.I make a specbond between ligand and residue, Is this bond proper for EM or MD simulation? What parameters are defined on it? if grompp doesn't complain there are parameters for angles and bonds etc. Use gmxdu

[gmx-users] about specbond

Dear all, I'm trying to run a simulation of a ligand bound to an enzyme.I make a specbond between ligand and residue, Is this bond proper for EM or MD simulation? What parameters are defined on it? Thank you in advance! ___ gmx-users mailing listg