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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@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-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@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? <9000...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Binding free energy of an ion from alchemical > transformation > Message-ID: > < > cak_bonfb_m2mgxumw8gswhfzbtdifp4lkjw4pgbhvy3p5uc...@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.t...@qut.edu.au> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] umbrella sampling tutorial > Message-ID: > < > dm2pr0101mb10690504f9ed567db577b697b6...@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.abra...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] enemat output > Message-ID: > < > camnumatrubz5arfdzcb-bz+1zrbdoqff68ahgw-iemicm7y...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On 11/03/2015 3:44 am, "Diogo Martins de S?" <sadi...@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-requ...@gromacs.org. > > > ------------------------------ > > Message: 4 > Date: Wed, 11 Mar 2015 15:01:29 +0530 > From: tasneem kausar <tasneemkausa...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] g_anaeig error > Message-ID: > <CAFaK4UZND1MO2bzEhAJJp9upAJJXDxk-V1UjcLU6W8m=- > re...@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 ." <sujithk...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Thermostats and MSD > Message-ID: > <CAKaGHgtCBQNJU2_YLPKX=dAimKJMVy= > s36carsstjbksuad...@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 <tsje...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] g_anaeig error > Message-ID: > < > cabze1sgyvzadcjsklrso84rwtfnjrm6ubjgk6txp34jn8kr...@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 < > tasneemkausa...@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-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > > ------------------------------ > > Message: 7 > Date: Wed, 11 Mar 2015 09:49:50 +0000 > From: Alexander Tzanov <alexander.tza...@csi.cuny.edu> > To: gmx-users <gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: "alex.tza...@csi.cuny.edu" <alex.tza...@csi.cuny.edu> > Subject: [gmx-users] Compiler > Message-ID: > <f5699b2497cefd418883db2ed5cfcb36e83ce...@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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 131, Issue 49 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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