Re: [gmx-users] Distance for window spacing in US?

potential of mean force along any direction. Thanks, Yun On Wed, Feb 20, 2013 at 1:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/13 11:01 AM, Yun Shi wrote: Hi Justin, I was not able to find relevant posts in the archive. Any special keyword for searching? I'm afraid I can't think

Re: [gmx-users] Protein unfolded after COM pulling

to the COM feel stronger force that the part of molecule that is far away from its COM? Thanks, Yun On Mon, Feb 4, 2013 at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/4/13 9:32 PM, Yun Shi wrote: Hi all, I am pulling one monomer of a tetrameric protein away from the other three monomers

Re: [gmx-users] Many energygrps to output

I guess I will do mdrun -rerun 400 times then. Thanks, Yun On Thu, Feb 7, 2013 at 9:06 PM, Bogdan Costescu bcoste...@gmail.com wrote: On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi yunsh...@gmail.com wrote: So instead of making an index file with 399 groups of each residue in A and typing

Re: [gmx-users] amber to gromacs error

On Sun, Dec 9, 2012 at 9:46 AM, Albert mailmd2...@gmail.com wrote: hello: I am using the command: acpype.py -p prmtop -x S13.rst to convert Amber system into Gromacs system, but it failed when I try to generate .tpr file: WARNING 1 [file prmtop_GMX.top, line 19]: Too few parameters

Re: [gmx-users] How to avoid adding ions close to ligand

anyone suggest a way around this? Thanks, Yun On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably

[gmx-users] How to delete atoms during MD runs?

Hi everyone, I am running MD of an enzyme containing co-factor FADH2. After the enzyme stabilize, I want to reduce the FADH2 to FAD, which for me is to delete two H atoms and change the topology file and .gro file correspondingly. However, I want to continue the MD run with the state

Re: [gmx-users] How to delete atoms during MD runs?

be an alternative way to look at the system evolution upon reduction of the co-factor? Thanks, Yun On Sat, Sep 8, 2012 at 3:17 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/09/2012 8:09 AM, Yun Shi wrote: Hi everyone, I am running MD of an enzyme containing co-factor FADH2. After the enzyme

Re: [gmx-users] rvdw and dispersion correction for amber99sb

mark.abra...@anu.edu.au wrote: On 21/08/2012 2:30 PM, Yun Shi wrote: Hello all, I am simulating protein-ligand complex with amber99sb force field in TIP3P water. What would be a reasonable value rvdw? I saw someone uses 1.0, and I did not find any abnormality when using 1.4 nm for rvdw

Re: [gmx-users] how to use the triplets index file generated by g_hbond

), but in the summary_HBmap.dat file there showed only 0.1 % Exist. of this specific H-bond. Anything wrong with my interpretation? Please see attached the files I used/ generated. Thanks, Yun On Sat, May 5, 2012 at 10:43 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/5/12 1:22 PM, Yun Shi wrote

[gmx-users] how to use the triplets index file generated by g_hbond

Hello all, I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor - Donor - Hydrogen in each line of the last index group. But I wonder I could I use this index file to monitor each hydrogen bond specified by these triplets along the trajectory? Also, I understand that

[gmx-users] how to g_select bound water molecules

Hello all, Can anyone tell me how to get in help examples in g_select by typing some commands? Anyway, I want to select bound waters between my ligand and protein using -select 'resname SOL within 0.5 ...'. Any idea? Thanks for any suggestion. Yun -- gmx-users mailing list

[gmx-users] Re: how to g_select bound water molecules

Never mind. I got it. On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi yunsh...@gmail.com wrote: Hello all, Can anyone tell me how to get in help examples in g_select by typing some commands? Anyway, I want to select bound waters between my ligand and protein using -select 'resname SOL within 0.5

Re: [gmx-users] Re: how to g_select bound water molecules

, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Yun Shi *Sent:* Tuesday, 3 April 2012 9:58 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Re: how to g_select bound water

[gmx-users] Scale down/ up velocities when coupling temperature and pressure?

Hi all, I am just wondering about how GROMACS works when coupling temperature and pressure. Assuming the simplest coupling method, like Berendsen, does GROMACS just scale down/ up kinetic energy (KE) for each particle in the system, such as KE1/KE2 = T1/T2 ? Similarly for pressure, KE1/KE2 =

[gmx-users] sudden jumps in RMSD etc.

Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then -fit

[gmx-users] what is a central structure

Hello everyone, I am using g_cluster with gromos method to do some clustering, and by default, -cl writes the central structure of each cluster obtained. So I wonder what 'central structure' mean? Assuming that I cluster based on RMSD values relative to the starting conformation, and that I then

Re: [gmx-users] nrexcl = 2 or 3?

Hi Mark, I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using

Re: [gmx-users] MD simulation of Glycoproteion

2011/12/14 陈应广 525342...@qq.com ** Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know

[gmx-users] how to edit a .xvg file?

Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. Thanks, Yun

Re: [gmx-users] how to edit a .xvg file?

From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] how to edit a .xvg file? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ecd8a11.9030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Yun Shi wrote: Hi everyone, I wonder

[gmx-users] Re: how to edit a .xvg file?

Sorry for this question. The bash script turned out to be a one-liner. Yun -- 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

[gmx-users] the force constant in constant speed umbrella pulling

Hi everyone, I am just wondering about the mathematical and physical meaning of this force constant when pulling a ligand from its receptor. So I can imagine a dummy atom is linked to the ligand via a spring, and it is moving away from the receptor at 1 nm/ns with the spring force constant 1000

[gmx-users] picking out resident water molecule?

Hi everyone, I am doing MD simulation with a protein-ligand system, and I want to pick out the water molecules (their residue numbers or coordinates in any frame) that simultaneously contact (within 0.4 nm range for heavy atoms) the ligand and the protein, so that I could plot the lifetime of

[gmx-users] Re: sudden drop of minimal periodic distance

contacts. Hope it helps, Tsjerk On Nov 10, 2011 1:45 AM, Yun Shi yunsh...@gmail.com wrote: Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm, the min periodic image dist still dropped abruptly to 0.172 or something like this after around 35 ns or 30 ns (different trajectory

Re: [gmx-users] where is Coul-LR?

So would it be reasonable to set rcoulomb = 2 or even 3 nm when rerunning a trajectory? I am looking at a ligand-antibody system, and I guess the long-range electrostatic interactions will not be small. A trick proposed by Nicolas in the mailing list during 2007 is to set charges to 0.00 for

[gmx-users] sudden drop of minimal periodic distance

Hello everyone, I am using g_mindist with -pi option to look at the minimal distance between periodic images of my protein-ligand system. It appears that after a certain amount of time (12 ns or 30 ns or ...), there would be a sudden drop of min distance from well above 2 nm to around 0.15 nm.

[gmx-users] Re: sudden drop of minimal periodic distance

with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi yunsh...@gmail.com wrote: Hello everyone, I am using g_mindist with -pi option to look at the minimal distance between periodic images of my protein-ligand system. It appears that after a certain amount of time (12 ns or 30 ns

[gmx-users] where is Coul-LR?

Hello all, I understand that setting rcoulomb rlist should give me Coul-LR from the .edr file. But I set rcoulomb = rlist since PME was used to calculate long range electrostatic interactions, and when I tried g_energy, I only have: 58 Coul-SR:Protein-LIG 59 LJ-SR:Protein-LIG

[gmx-users] fudge QQ values

Hello everyone, I just have a quick question. So the fudgeQQ value for amber99sb force field in gromacs is 0.8333, but I wonder if we should use 0.83 or 0.8333? I quite different simulation results by manipulating this value. In my antibody - ligand system, 0.8333 showed ligand not

Re: [gmx-users] Thioester bond problem

Hi Alberto, I used a stupid method to deal with this kind of non-standard moiety. You can use AmberTools to parameterize your thioester, together with your proteins, and then use acpype to convert they topology and coordinate files to gromacs format. But I am not sure if you want to use amber

[gmx-users] position restraints on heavy atoms or all?

Hello all, I am using amber99SB to model an antibody with organic ligands. I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is aimed at getting the temperature and

[gmx-users] would trjcat correctly delete extra frames?

Hi all, I am doing simulations on cluster piece by piece with -maxh and -noappend options of mdrun. However, one piece crushed way before approaching the max hours for unknown reasons. As a result, the part0004.trr file contains a couple of frames ahead of part0004.cpt file, since the most .cpt

[gmx-users] Re: reasons for slow computation?

than the other since the distance is smaller. So should I be able to compare any averaged, or say, clustered properties? Thanks, Yun On 11/10/2011 1:40 PM, Yun Shi wrote: Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. More likely

[gmx-users] reasons for slow computation?

Hi all, I am doing MD simulation on two almost identical protein-ligand systems with GROMACS4.5.4 and amber99SB force fields. Almost every single parameter I used for this two systems are the same (I literally copied the mdp files for both), except that one has 65235 atoms while the other has

[gmx-users] Re: reasons for slow computation?

And another difference I noticed from .log files are: .. Initial maximum inter charge-group distances: two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808 multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808 Minimum cell size due to bonded

[gmx-users] not guaranteed to be binary identical ?

Hi all, I am doing my MD simulations piece by piece, with -maxh and -noappend options, so that I can link pieces of trajectories together afterward. But as I did part0001 with 48 cores, and part0002 with 72 cores, the log file told me that: #nodes mismatch, current program: 72

Re: [gmx-users] Re: reasons for slow computation?

Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. But I am still wondering that, would the difference in initial maximum inter charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD gird (0.620nm vs 0.618nm) make

Re: [gmx-users] acpype generated different tip3p water paramters

Hi Alan, So is acpype using a conversion factor of 4.184 for dihedral force constant? I found some dihedral constants as 0.156 in the amber format, which should be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force constant of 0.65084 after conversion, which is slightly off. I

[gmx-users] different tip3p water parameters between AMBER and GROMACS

Hi all, I found that the 99SB force field in AMBERTOOLS1.5 and GROMACS4.5.4 have different force constants for bond and angle parameters, after converting them to the same unit. So for those in AMBER [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr

[gmx-users] acpype generated different tip3p water paramters

Hi all, I just noted that the tip3p water converted from amber format to gromacs format is [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834

Re: [gmx-users] different sets of fudgeQQ and fudgeLJ

...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 18/09/2011 8:58 AM, Yun Shi wrote: Hi all, I want to apply different values of LJ and QQ scaling factors for two interacting molecules A and B. Since I already have the .itp files for each molecule, should I just add

[gmx-users] Re: different sets of fudgeQQ and fudgeLJ

Hi Mark and Justin, I think I should be more specific here. So i.e., I want to study the interaction between a protein receptor and a carbohydrate ligand with MD simulation, and I plan to use ff99sb for protein while glycam06 for carbohydrate. Since the two force fields are parameterized using

[gmx-users] different sets of fudgeQQ and fudgeLJ

Hi all, I want to apply different values of LJ and QQ scaling factors for two interacting molecules A and B. Since I already have the .itp files for each molecule, should I just add something like: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1

[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

and compare against one step EM with GMX. Do the proper conversions and Energies diff should be 0.001%. Cheers, Alan On 12 September 2011 21:21, Yun Shi yunsh...@gmail.com wrote: Hi all, I am not a CS person, but I did find something in acpype.py as . if phase

[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

Hi all, I am not a CS person, but I did find something in acpype.py as . if phase in [0, 180]: properDihedralsGmx45.append([item[0].atoms, phaseRaw, kPhi, period]) if not self.gmx45: if kPhi 0: V[period]

[gmx-users] amb2gmx.pl to convert GLYCAM topology

Hi all, I understand this problem has been discussed before, but it seems no conclusion has been drawn. GLYCAM force field assigns negative force constants to some dihedrals, and when amb2gmx.pl was used to convert prmtop file to gromacs top file, these negative values seem to be ignored. Some

[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

Hi Alan, I am not sure if my acpype version is not updated. But I did try, and it behaved the same as amb2gmx.pl for dihedrals. Yun Or why not trying acpype? Cheers, Alan On 9 September 2011 07:37, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/09/2011 4:21 PM, Yun Shi wrote: Hi all

[gmx-users] missing parameters in auto-generated topology file?

Hi all, I used pdb2gmx and selected amber99sb for generation of itp files of a normal peptide within GROMACS 4.5.4. But I saw that all the bonds, angles, and dihedral parameters (c0, c1, c2 ...) were not present in the itp file, while only funct is defined. It seems the same thing happens with

[gmx-users] gd_29 or gd_41 ?

- 0.9 ; ... Thanks, Yun Shi -- 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. Use the www

[gmx-users] Re: gd_29 or gd_41 ?

definition? Thanks, Yun Shi On Wed, Aug 24, 2011 at 3:00 PM, Yun Shi yunsh...@gmail.com wrote: Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000

[gmx-users] sugar dihedral parameters

use? Thanks, Yun Shi -- 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. Use the www interface

[gmx-users] parameters for CH1 -- S -- CH2 ?

Hi all, I have a small molecule with a part like: CH1 --- CH1 --- S --- CH2 --- CH1 | CH1 I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and dihedral parameters according what are already present in the gromos53a6.ff/ffbonded.itp file. Since this

[gmx-users] validation of ligand parameters

this. The command g_chi only computes NMR 3J coupling constants for amino acid backbond and sidechain atoms? Thanks for any suggestion! Yun Shi -- 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

[gmx-users] To modify PRODRG-generated .itp file?

Hi all, In addition to modifying atomic charges to the .itp file generated by PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4 LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ interactions) with the vdw C12 and C6 parameters I prefer. So should

[gmx-users] LINCS with amber99SB ?

(or if they are all good enough) and computational costs of these options above. And maybe I should ask this question in the developers mailing list, but would GROMACS support SHAKE in parallel in the near future, like in a 4.5.5 version? Thanks a lot, Yun Shi -- gmx-users mailing listgmx-users

[gmx-users] Re: LINCS with amber99SB ?

, it is always OK to use LINCS rather than SHAKE, right? And for those bonds not constrained when using amber99sb force field, would GROMACS automatically apply the harmonic bond stretching functional form as specified in the [ bonds ] section of corresponding .itp files? Regards, Yun Yun Shi wrote: Hi

Re: Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

, and then modify the atomic charges according to the 56ACARBO paper? Thanks, Yun Shi Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

contain all those C12 and C6 LJ parameters already? Or mdrun need to retrieve these parameters according to the atom types from corresponding files within the gromos53a6.ff folder? Regards, Yun Shi Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you

[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

for any explanation and suggestion. Yun Shi -- 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] setting vdw cutoff with specific force-filed?

cancel out each other? Thanks a lot, Yun Shi On 04/08/11, Justin A. Lemkul jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper

[gmx-users] Re: setting vdw cutoff with specific force-filed?

Hi Justin, I got it now. During the 10fs, even water molecules with a speed of 500 m/s only have a 0.005 nm displacement, which is far less than than 0.9 nm or 1.4 nm. Thanks again! Yun Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van

[gmx-users] setting vdw cutoff with specific force-filed?

, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? Any suggestion would be appreciated! Thanks, Yun Shi -- gmx-users mailing listgmx

[gmx-users] How to protonate a gmx trajectory?

Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system. I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir nor not found