[gmx-users] On dihedral type for CHARMM

Hi everyone!   I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the manual. I read that there are 9 supported

Re: [gmx-users] On dihedral type for CHARMM

On 10/04/2011 4:12 PM, Mr Bernard Ramos wrote: Hi everyone! I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the

[gmx-users] Extending Simulation

Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run

Re: [gmx-users] Extending Simulation

On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4

[gmx-users] NPT.mdp parameters NOTE

Dear Dr.Justin As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file. You have used tau-t = 0.1 in most of your md.mdp files for generating npt ensemble. When I use a npt file with these settings,there is a Note as following: sorry,i can't

Re: [gmx-users] Extending Simulation

Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation.

Re: [gmx-users] Extending Simulation

On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to

Re: [gmx-users] Extending Simulation

Dear Dr.Mark Thank you very much you are right I understood your mean exactly, On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham

[gmx-users] converging value

Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. can everybody guide me? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle

Re: [gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

On 2011-04-10 11.11, sa wrote: Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so

Re: [gmx-users] NPT.mdp parameters NOTE

He told me you can use up to 0.5 in an off-list email and in fact, does so in the KALP-15 in DPPC example... On 2011-04-10 02:54:15AM -0500, mohsen ramezanpour wrote: Dear Dr.Justin As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file.

Re: [gmx-users] converging value

On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. Longer simulations on bigger systems. Mark -- gmx-users

Re: [gmx-users] Dangling bond error for dna

majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the

[gmx-users] probelm of using amber force field

Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and

Re: [gmx-users] probelm of using amber force field

fancy2012 wrote: Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the

Re: [gmx-users] converging value

Dear Dr.Mark thank you for your attention How long is enough? for example I have run 200 ps for making npt(p=1 bar) for my system (300 nm^3) But the pressure is oscilating so much,and I can't be sure if it has converged or not! of course its average is approximately 5 bar (at the end of log file)

Re: [gmx-users] converging value

On 10/04/2011 9:41 PM, mohsen ramezanpour wrote: Dear Dr.Mark thank you for your attention How long is enough? For example, when the size of error estimate reported by g_energy is smaller than the quantity you are trying to observe. That might take many nanoseconds in the case of

Re: [gmx-users] Error while performing a REMD simulation

2011/4/10 Mark Abraham mark.abra...@anu.edu.au: On 10/04/2011 11:44 AM, Justin A. Lemkul wrote: Maybe this is unrelated to the underlying problem, but hopefully it helps in the long run.  Nothing worse than a reviewer saying, Nice project, but 100% of the data are junk. Bad idea, and 100%

Re: [gmx-users] Error while performing a REMD simulation

2011/4/10 Mark Abraham mark.abra...@anu.edu.au: On 10/04/2011 10:58 AM, devicerandom wrote: A polite request for correct behaviour is suitable. Use of ALL CAPS is also a breach of netiquette. :-) Ouch. I just wanted to convey strength, it's not like I WROTE ALL THE MAIL IN ALL CAPS :-)

[gmx-users] converging value

You need to look at the dependence of the statistical value (in this case the average pressure) with (a) increasing equilibration time that you discard prior to collecting pressure data, and (b) increasing production simulation time that you include in your average. Create the first plot,

[gmx-users] Re:gmx-users Digest, Vol 84, Issue 81

very much in advance! -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/b7b8202b/attachment-0001.html

Re: [gmx-users] Dangling bond error for dna

Okay, thank you. I'll try to fix it. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 4:17:59 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

Thank you David A bientôt SA -- Message: 1 Date: Sun, 10 Apr 2011 11:17:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM and

Re: [gmx-users] Dangling bond error for dna

Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3. Thanks, Majid From: Justin A. Lemkul

Re: [gmx-users] Dangling bond error for dna

Okay, I am trying AmberTools as well. Thanks Justin! Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 10:16:57 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Is

[gmx-users] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can

Dear gmxers, I have had tried to install gmx-4.5.4 by compiling the source code. The first step ./configure finished without any error, but the second step running make reported some errors as follows /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:

Re: [gmx-users] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can

Dear gmxers, I have had tried to install gmx-4.5.4 by compiling the source code. The first step ./configure finished without any error, but the second step running make reported some errors as follows /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:

[gmx-users] mdrun segmentation fault

Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20

[gmx-users] comm-grps for a membrane-protein-ligand system

Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to

Re: [gmx-users] mdrun segmentation fault

Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20

Re: [gmx-users] 1,5 and 1,6 LJ interactions for OPLS AA SEI

Hi everyone! The OPLS AA SEI for carbohydrates scales the 1,5 and 1,6 interaction by a certain factor. How do I go about introducing the scaling of these intearctions in the ff parameters? The CHARMM ff also has certain 1,4 parameters, I am not sure how we can go about placing these specific