[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 49
tasneem kausar
tasneemkausar12 at gmail.com
Wed Mar 11 11:46:11 CET 2015
for PCA i used the g_covar followed by g_anaeig.
i used the command line for g_covr as
g_covar -f full.xtc -s full.tpr -o eig.xvg
I have selected the protein for least square fit and main chain for
covarience analysis.
There is a warning message.
WARNING: number of atoms in tpx (312) and trajectory (1061) do not match
The abve comman gave the files average.pdb, eigenvec.trr and eig.xvg
Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
The commnan line for g_anaeig is given below.
g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
For least square fit i have selected the protein and same for the
eigenvectors
This gave the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?
On Wed, Mar 11, 2015 at 3:31 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Binding free energy of an ion from alchemical transformation
> (Wojciech Kope?)
> 2. umbrella sampling tutorial (Ming Tang)
> 3. Re: enemat output (Mark Abraham)
> 4. g_anaeig error (tasneem kausar)
> 5. Thermostats and MSD (sujithkakkat .)
> 6. Re: g_anaeig error (Tsjerk Wassenaar)
> 7. Compiler (Alexander Tzanov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Mar 2015 09:23:53 +0100
> From: Wojciech Kope? <9000nin at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Binding free energy of an ion from alchemical
> transformation
> Message-ID:
> <
> CAK_bONfB_m2MgxUMW8gSwHfzBtdiFP4LkJW4PGbHVy3P5uc3jw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I'm thinking about performing free energy calculations for a protein that
> binds cations, using alchemical transformation method. In the simplest
> case I'd transform an ion (one atom) into a naked particle; however in this
> case I'd get a non-zero overall charge of the system during the charge
> decoupling. I'm aware of some corrections for that and also that Gromacs
> probably neutralises the charge with PME (?). Another approach I've been
> thinking of is to simultaneously couple a naked particle somewhere in the
> bulk with the environment, switching on the charge in a same way as the
> charge of the ion is being switched off. In this way, the charge would be 0
> all the time, and at the end of the simulation would yield the protein with
> an empty binding site and the ion somewhere in the bulk. Are there any
> obvious pitfalls with this approach?
>
> Thank you,
> Wojciech
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Mar 2015 08:17:42 +0000
> From: Ming Tang <m21.tang at qut.edu.au>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] umbrella sampling tutorial
> Message-ID:
> <
> DM2PR0101MB10690504F9ED567DB577B697B6190 at DM2PR0101MB1069.prod.exchangelabs.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I was learning the Umbrella Sampling tutorial step by step on Gromacs
> 5.0.4.
> Everything was fine until I got to the step five (run the continuous
> pulling simulation).
> Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
> failed.
>
> ; Pull code in tutorial
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = Chain_B
> pull_group1 = Chain_A
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
>
> ; COM pulling I modified
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_coord1-groups = 2
> pull-group1-name = Chain_B
> pull_group2-name = Chain_A
> pull-coord1-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k = 1000 ; kJ mol^-1 nm^-2
>
> Fatal error:
> Group Chain_B referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> Index:
> [ r_1-27 ]
> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
> 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
> 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
> 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
> 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
> 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
> 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
> 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
> 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
> 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
> 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
> 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
> 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
> 226
> [ r_28-54 ]
> 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241
> 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256
> 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271
> 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286
> 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301
> 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316
> 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331
> 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346
> 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361
> 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376
> 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391
> 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406
> 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421
> 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436
> 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451
> 452
>
> Could anybody tell me what's wrong with the COM pulling code I modified?
>
> Thanks in advance!
>
> Regards,
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 11 Mar 2015 09:35:57 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] enemat output
> Message-ID:
> <
> CAMNuMATrUbZ5ARfdzcB-bz+1zRBDoqFF68ahGW-iEmicM7y8iw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On 11/03/2015 3:44 am, "Diogo Martins de S?" <sadiogo at mol.bio.br> wrote:
> >
> > Hi guys,
> >
> > Can any one show a picture of how a normal enemat output should look
> > like?
> >
> > Since the bug in enemat was only fixed in version 4.6.5, I have a very
> > basic question:
> >
> > Can I install a newer version of gromac (say 5) and use its enemat to
> > treat .edr files from older versions (i.e. 4.5.3 and 4.6.3)??
>
> Yes
>
> Mark
>
> > Many thanks
> >
> > Diogo
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Mar 2015 15:01:29 +0530
> From: tasneem kausar <tasneemkausar12 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] g_anaeig error
> Message-ID:
> <CAFaK4UZND1MO2bzEhAJJp9upAJJXDxk-V1UjcLU6W8m=-
> REguQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> for PCA i used the g_covar followed by g_anaeig.
> for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
> these files are generated by g_covar.
> g_anaeig gives the following message;
> There were 40 inconsistent shifts. Check your topology
> where is the problem occured?
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 11 Mar 2015 15:12:09 +0530
> From: "sujithkakkat ." <sujithks58 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Thermostats and MSD
> Message-ID:
> <CAKaGHgtCBQNJU2_YLPKX=dAimKJMVy=
> s36cArSStJBksUADnmg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>
> I am simulating a system of small hydrophobic solutes ( CH4) dissolved
> in water. Simulations are performed in the NPT simulation, and I would like
> to determine the diffusion coefficients from MSD plots. I have two related
> questions;
>
> (1) Is the thermostat going to seriously affect the diffusivity of the
> molecules. I am using Nose-Hoover thermostat with a time constant of 0.2
> ps. Is the choice of time constant very crucial while studying diffusivity.
> Should I avoid thermostat and go for NVE simulations for studying
> diffusivity.
>
> (2) From radial distribution functions, it is found that there is
> association between the hydrophobic solvents. I would like to know, if in
> case a small cluster of the hydrophobic solutes are formed, then the
> whether the rotational motion of these clusters contribute to dispalcement
> in the MSD calculation.
>
> Please comment.
>
> Regards,
> Sujith.
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 11 Mar 2015 10:51:13 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] g_anaeig error
> Message-ID:
> <
> CABzE1SgyVZaDcJskLrsO84rwTfNjRm6ubJgk6tXp34Jn8kr06A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Tasneem,
>
> Please provide a complete workflow, with commands and selections.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Mar 11, 2015 at 10:31 AM, tasneem kausar <
> tasneemkausar12 at gmail.com>
> wrote:
>
> > for PCA i used the g_covar followed by g_anaeig.
> > for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
> > these files are generated by g_covar.
> > g_anaeig gives the following message;
> > There were 40 inconsistent shifts. Check your topology
> > where is the problem occured?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 11 Mar 2015 09:49:50 +0000
> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu>
> To: gmx-users <gromacs.org_gmx-users at maillist.sys.kth.se>
> Cc: "Alex.tzanov at csi.CUNY.edu" <Alex.tzanov at csi.CUNY.edu>
> Subject: [gmx-users] Compiler
> Message-ID:
> <F5699B2497CEFD418883DB2ED5CFCB36E83CE94C at MBOX1.FLAS.CSI.CUNY.EDU>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all I am trying to install the 5.0.4 with GPU support with Intel 15
> compiler and 1.8.4 openmpi.I got errors that only Intel 14 is supported.
> Is this true? And if so do you plan to have tested/port GMX with latest
> Intel compiler?
>
> Thanks Alex
>
> ________________________________
> Connect with CSI on Social Media><http://csitoday.com/social_media/>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 131, Issue 49
> ******************************************************
>
More information about the gromacs.org_gmx-users
mailing list